diff --git a/xml_converter/generators/code_generator.py b/xml_converter/generators/code_generator.py
index c35fc1d1..dbd5c683 100644
--- a/xml_converter/generators/code_generator.py
+++ b/xml_converter/generators/code_generator.py
@@ -506,6 +506,7 @@ def generate_cpp_variable_data(
             cpp_includes.hpp_relative_includes.add("icon_gen.hpp")
             cpp_includes.hpp_relative_includes.add("trail_gen.hpp")
 
+            cpp_includes.cpp_absolute_includes.add("utility")
             cpp_includes.cpp_absolute_includes.add("type_traits")
 
         for filepath, document in sorted(self.data.items()):
diff --git a/xml_converter/generators/cpp_templates/class_template.cpp b/xml_converter/generators/cpp_templates/class_template.cpp
index 51932b58..2cf0f2d2 100644
--- a/xml_converter/generators/cpp_templates/class_template.cpp
+++ b/xml_converter/generators/cpp_templates/class_template.cpp
@@ -93,7 +93,12 @@ vector<string> {{cpp_class}}::as_xml() const {
     return xml_node_contents;
 }
 
-waypoint::{{cpp_class}} {{cpp_class}}::as_protobuf() const {
+{% if cpp_class == "Category": %}
+    waypoint::{{cpp_class}} {{cpp_class}}::as_protobuf(string full_category_name, map<string, vector<Parseable*>>* parsed_pois) const {
+        full_category_name += this->name;
+{% else %}
+    waypoint::{{cpp_class}} {{cpp_class}}::as_protobuf() const {
+{% endif %}
     waypoint::{{cpp_class}} proto_{{cpp_class_header}};
     {% if cpp_class == "Icon": %}
         waypoint::Trigger* trigger = nullptr;
@@ -146,8 +151,24 @@ waypoint::{{cpp_class}} {{cpp_class}}::as_protobuf() const {
         }
     {% endif %}
     {% if cpp_class == "Category": %}
+
+        auto pois = parsed_pois->find(full_category_name);
+
+        if (pois != parsed_pois->end()) {
+            for (unsigned int i = 0; i < pois->second.size(); i++) {
+                if (pois->second[i]->classname() == "POI") {
+                    Icon* icon = dynamic_cast<Icon*>(pois->second[i]);
+                    proto_{{cpp_class_header}}.add_icon()->MergeFrom(icon->as_protobuf());
+                }
+                else if (pois->second[i]->classname() == "Trail") {
+                    Trail* trail = dynamic_cast<Trail*>(pois->second[i]);
+                    proto_{{cpp_class_header}}.add_trail()->MergeFrom(trail->as_protobuf());
+                }
+            }
+        }
+
         for (const auto& [key, val] : this->children) {
-            waypoint::{{cpp_class}} proto_{{cpp_class_header}}_child = val.as_protobuf();
+            waypoint::{{cpp_class}} proto_{{cpp_class_header}}_child = val.as_protobuf(full_category_name + ".", parsed_pois);
             proto_{{cpp_class_header}}.add_children()->CopyFrom(proto_{{cpp_class_header}}_child);
         }
     {% endif %}
diff --git a/xml_converter/generators/cpp_templates/class_template.hpp b/xml_converter/generators/cpp_templates/class_template.hpp
index 19d7aa26..72102bf5 100644
--- a/xml_converter/generators/cpp_templates/class_template.hpp
+++ b/xml_converter/generators/cpp_templates/class_template.hpp
@@ -34,7 +34,11 @@ class {{cpp_class}} : public Parseable {
     virtual std::vector<std::string> as_xml() const;
     virtual std::string classname();
     bool init_xml_attribute(rapidxml::xml_attribute<>* attribute, std::vector<XMLError*>* errors, std::string base_dir = "");
-    waypoint::{{cpp_class}} as_protobuf() const;
+    {% if cpp_class == "Category": %}
+        waypoint::{{cpp_class}} as_protobuf(std::string full_category_name, std::map<std::string, std::vector<Parseable*>>* parsed_pois) const;
+    {% else: %}
+        waypoint::{{cpp_class}} as_protobuf() const;
+    {% endif %}
     void parse_protobuf(waypoint::{{cpp_class}} proto_{{cpp_class_header}});
     {% if attributes_of_type_marker_category %}
         bool validate_attributes_of_type_marker_category();
diff --git a/xml_converter/proto/waypoint.proto b/xml_converter/proto/waypoint.proto
index 33545ca2..ab239d57 100644
--- a/xml_converter/proto/waypoint.proto
+++ b/xml_converter/proto/waypoint.proto
@@ -4,8 +4,6 @@ package waypoint;
 
 message Waypoint {
     repeated Category category = 1;
-    repeated Icon icon = 2;
-    repeated Trail trail = 3;
 }
 
 message Category {
@@ -15,10 +13,11 @@ message Category {
     string name = 4;
     string tip_description = 5;
     repeated Category children = 6;
+    repeated Icon icon = 7;
+    repeated Trail trail = 8;
 }
 
 message Icon {
-    Category category = 1;
     TexturePath texture_path = 2;
     GUID guid = 3;
     int32 map_id = 4;
@@ -53,10 +52,10 @@ message Icon {
     bool tentative__render_on_minimap = 2051;
     string bhdraft__schedule = 2052;
     float bhdraft__schedule_duration = 2053;
+    Category category = 2054;
 }
 
 message Trail {
-    Category category = 1;
     TexturePath texture_path = 2;
     GUID guid = 3;
     int32 map_id = 4;
@@ -85,6 +84,7 @@ message Trail {
     bool tentative__render_on_minimap = 2051;
     string bhdraft__schedule = 2052;
     float bhdraft__schedule_duration = 2053;
+    Category category = 2054;
 }
     
 message TexturePath {
diff --git a/xml_converter/src/category_gen.cpp b/xml_converter/src/category_gen.cpp
index 392eff0b..f480a007 100644
--- a/xml_converter/src/category_gen.cpp
+++ b/xml_converter/src/category_gen.cpp
@@ -4,6 +4,7 @@
 #include <iosfwd>
 #include <string>
 #include <type_traits>
+#include <utility>
 
 #include "attribute/bool.hpp"
 #include "attribute/string.hpp"
@@ -94,7 +95,8 @@ vector<string> Category::as_xml() const {
     return xml_node_contents;
 }
 
-waypoint::Category Category::as_protobuf() const {
+waypoint::Category Category::as_protobuf(string full_category_name, map<string, vector<Parseable*>>* parsed_pois) const {
+    full_category_name += this->name;
     waypoint::Category proto_category;
     if (this->default_visibility_is_set) {
         proto_category.set_default_visibility(this->default_visibility);
@@ -111,8 +113,24 @@ waypoint::Category Category::as_protobuf() const {
     if (this->tooltip_description_is_set) {
         proto_category.set_tip_description(this->tooltip_description);
     }
+
+    auto pois = parsed_pois->find(full_category_name);
+
+    if (pois != parsed_pois->end()) {
+        for (unsigned int i = 0; i < pois->second.size(); i++) {
+            if (pois->second[i]->classname() == "POI") {
+                Icon* icon = dynamic_cast<Icon*>(pois->second[i]);
+                proto_category.add_icon()->MergeFrom(icon->as_protobuf());
+            }
+            else if (pois->second[i]->classname() == "Trail") {
+                Trail* trail = dynamic_cast<Trail*>(pois->second[i]);
+                proto_category.add_trail()->MergeFrom(trail->as_protobuf());
+            }
+        }
+    }
+
     for (const auto& [key, val] : this->children) {
-        waypoint::Category proto_category_child = val.as_protobuf();
+        waypoint::Category proto_category_child = val.as_protobuf(full_category_name + ".", parsed_pois);
         proto_category.add_children()->CopyFrom(proto_category_child);
     }
     return proto_category;
diff --git a/xml_converter/src/category_gen.hpp b/xml_converter/src/category_gen.hpp
index 3ef42874..89e7a96c 100644
--- a/xml_converter/src/category_gen.hpp
+++ b/xml_converter/src/category_gen.hpp
@@ -32,6 +32,6 @@ class Category : public Parseable {
     virtual std::vector<std::string> as_xml() const;
     virtual std::string classname();
     bool init_xml_attribute(rapidxml::xml_attribute<>* attribute, std::vector<XMLError*>* errors, std::string base_dir = "");
-    waypoint::Category as_protobuf() const;
+    waypoint::Category as_protobuf(std::string full_category_name, std::map<std::string, std::vector<Parseable*>>* parsed_pois) const;
     void parse_protobuf(waypoint::Category proto_category);
 };
diff --git a/xml_converter/src/xml_converter.cpp b/xml_converter/src/xml_converter.cpp
index 1617b099..225819ba 100644
--- a/xml_converter/src/xml_converter.cpp
+++ b/xml_converter/src/xml_converter.cpp
@@ -104,27 +104,31 @@ void remove_proto_child(waypoint::Category* proto_category, set<string> categori
 }
 
 void write_protobuf_file(string proto_directory, map<string, Category>* marker_categories, vector<Parseable*>* parsed_pois) {
-    // Creates a Waypoint message that contains all categories
-    waypoint::Waypoint all_categories;
-    for (const auto& category : *marker_categories) {
-        waypoint::Category proto_category = category.second.as_protobuf();
-        all_categories.add_category()->CopyFrom(proto_category);
-    }
-
     waypoint::Waypoint proto_pois;
     // Collects a set of map ids from Icon and Trail data
     std::set<int> map_ids;
     ofstream trail_data_file;
+    map<string, vector<Parseable*>> map_of_pois;
     for (const auto& parsed_poi : *parsed_pois) {
         if (parsed_poi->classname() == "POI") {
             Icon* icon = dynamic_cast<Icon*>(parsed_poi);
             map_ids.insert(icon->map_id);
+            map_of_pois[icon->category.category].push_back(icon);
         }
         else if (parsed_poi->classname() == "Trail") {
             Trail* trail = dynamic_cast<Trail*>(parsed_poi);
             map_ids.insert(trail->map_id);
+            map_of_pois[trail->category.category].push_back(trail);
         }
     }
+
+    // Creates a Waypoint message that contains all categories
+    waypoint::Waypoint all_categories;
+    for (const auto& category : *marker_categories) {
+        waypoint::Category proto_category = category.second.as_protobuf("", &map_of_pois);
+        all_categories.add_category()->CopyFrom(proto_category);
+    }
+
     waypoint::Waypoint output_message;
     std::set<string> categories_to_retain;
     for (int map_id : map_ids) {
@@ -138,15 +142,12 @@ void write_protobuf_file(string proto_directory, map<string, Category>* marker_c
                 Icon* icon = dynamic_cast<Icon*>(parsed_poi);
                 if (icon->map_id == map_id) {
                     populate_categories_to_retain(icon->category.category, &categories_to_retain);
-                    output_message.add_icon()->MergeFrom(icon->as_protobuf());
                 }
             }
             else if (parsed_poi->classname() == "Trail") {
                 Trail* trail = dynamic_cast<Trail*>(parsed_poi);
                 if (trail->map_id == map_id) {
                     populate_categories_to_retain(trail->category.category, &categories_to_retain);
-                    waypoint::Trail proto_trail = trail->as_protobuf();
-                    output_message.add_trail()->MergeFrom(proto_trail);
                 }
             }
         }
@@ -248,22 +249,6 @@ vector<Parseable*> parse_pois(rapidxml::xml_node<>* root_node, map<string, Categ
     return markers;
 }
 
-vector<Parseable*> parse_proto_pois(waypoint::Waypoint proto_message) {
-    vector<Parseable*> markers;
-
-    for (int i = 0; i < proto_message.icon_size(); i++) {
-        Icon* icon = new Icon();
-        icon->parse_protobuf(proto_message.icon(i));
-        markers.push_back(icon);
-    }
-    for (int i = 0; i < proto_message.trail_size(); i++) {
-        Trail* trail = new Trail();
-        trail->parse_protobuf(proto_message.trail(i));
-        markers.push_back(trail);
-    }
-    return markers;
-}
-
 void parse_marker_categories(rapidxml::xml_node<>* node, map<string, Category>* marker_categories, vector<XMLError*>* errors, int depth = 0) {
     if (get_node_name(node) == "MarkerCategory") {
         string name = lowercase(find_attribute_value(node, "name"));
@@ -278,12 +263,31 @@ void parse_marker_categories(rapidxml::xml_node<>* node, map<string, Category>*
         errors->push_back(new XMLNodeNameError("Unknown MarkerCategory Tag", node));
     }
 }
-void parse_proto_marker_categories(::waypoint::Category proto_category, map<string, Category>* marker_categories) {
-    string name = proto_category.name();
-    Category* this_category = &(*marker_categories)[name];
+
+void parse_waypoint_categories(string full_category_name, ::waypoint::Category proto_category, map<string, Category>* marker_categories, vector<Parseable*>* parsed_pois) {
+    full_category_name += proto_category.name();
+    Category* this_category = &(*marker_categories)[full_category_name];
     this_category->parse_protobuf(proto_category);
+
+    for (int i = 0; i < proto_category.icon_size(); i++) {
+        Icon* icon = new Icon();
+        icon->parse_protobuf(proto_category.icon(i));
+        // TODO: The field category in Icon is being deprciated
+        // This overwrites any icon.category with its position in the heirarchy
+        icon->category.category = full_category_name;
+        parsed_pois->push_back(icon);
+    }
+    for (int i = 0; i < proto_category.trail_size(); i++) {
+        Trail* trail = new Trail();
+        trail->parse_protobuf(proto_category.trail(i));
+        // TODO: The field category in Trail is being deprciated
+        // This overwrites any trail.category with its position in the heirarchy
+        trail->category.category = full_category_name;
+        parsed_pois->push_back(trail);
+    }
+
     for (int i = 0; i < proto_category.children_size(); i++) {
-        parse_proto_marker_categories(proto_category.children(i), &(this_category->children));
+        parse_waypoint_categories(full_category_name + ".", proto_category.children(i), &(this_category->children), parsed_pois);
     }
 }
 
@@ -335,10 +339,8 @@ void read_protobuf_file(string proto_filepath, map<string, Category>* marker_cat
     infile.open(proto_filepath, ios::in | ios::binary);
     proto_message.ParseFromIstream(&infile);
     for (int i = 0; i < proto_message.category_size(); i++) {
-        parse_proto_marker_categories(proto_message.category(i), marker_categories);
+        parse_waypoint_categories("", proto_message.category(i), marker_categories, parsed_pois);
     }
-    vector<Parseable*> temp_vector = parse_proto_pois(proto_message);
-    move(temp_vector.begin(), temp_vector.end(), back_inserter(*parsed_pois));
 }
 
 bool filename_comp(string a, string b) {
@@ -506,24 +508,23 @@ int main() {
     cout << "The protobuf write function took " << ms << " milliseconds to run" << endl;
 
     ////////////////////////////////////////////////////////////////////////////
-    // This section tests that the protobuf file can be parsed back to xml
+    // This section can test that a protobuf file can be parsed back to xml
     ////////////////////////////////////////////////////////////////////////////
-    parsed_pois.clear();
-    marker_categories.clear();
-
-    begin = chrono::high_resolution_clock::now();
-    read_protobuf_file("./protobins/50.data", &marker_categories, &parsed_pois);
-    end = chrono::high_resolution_clock::now();
-    dur = end - begin;
-    ms = std::chrono::duration_cast<std::chrono::milliseconds>(dur).count();
-    cout << "The protobuf read function took " << ms << " milliseconds to run" << endl;
-
-    begin = chrono::high_resolution_clock::now();
-    write_xml_file("./protobins/50.xml", &marker_categories, &parsed_pois);
-    end = chrono::high_resolution_clock::now();
-    dur = end - begin;
-    ms = std::chrono::duration_cast<std::chrono::milliseconds>(dur).count();
-    cout << "The xml write function took " << ms << " milliseconds to run" << endl;
+    // parsed_pois.clear();
+    // marker_categories.clear();
+    // begin = chrono::high_resolution_clock::now();
+    // read_protobuf_file("./protobins/1.data", &marker_categories, &parsed_pois);
+    // end = chrono::high_resolution_clock::now();
+    // dur = end - begin;
+    // ms = std::chrono::duration_cast<std::chrono::milliseconds>(dur).count();
+    // cout << "The protobuf read function took " << ms << " milliseconds to run" << endl;
+
+    // begin = chrono::high_resolution_clock::now();
+    // write_xml_file("./protobins/1.xml", &marker_categories, &parsed_pois);
+    // end = chrono::high_resolution_clock::now();
+    // dur = end - begin;
+    // ms = std::chrono::duration_cast<std::chrono::milliseconds>(dur).count();
+    // cout << "The xml write function took " << ms << " milliseconds to run" << endl;
 
     return 0;
 }