diff --git a/src/map/include/computeMap.hpp b/src/map/include/computeMap.hpp
index 562713d9..725d4a4c 100644
--- a/src/map/include/computeMap.hpp
+++ b/src/map/include/computeMap.hpp
@@ -721,21 +721,6 @@ namespace skch
 
           aggregator.join();
 
-          // Filter mappings for this subset to reduce memory usage
-          for (auto& [querySeqId, mappings] : combinedMappings) {
-              if (param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE) {
-                  MappingResultsVector_t filteredMappings;
-                  filterByGroup(mappings, filteredMappings, param.numMappingsForSegment - 1, false, *idManager, progress);
-                  mappings = std::move(filteredMappings);
-                  
-                  // Also apply length and identity filters
-                  filterWeakMappings(mappings, std::floor(param.block_length / param.segLength));
-                  if (param.filterLengthMismatches) {
-                      filterFalseHighIdentity(mappings);
-                  }
-                  sparsifyMappings(mappings);
-              }
-          }
 
           // Reset flags and clear aggregatedMappings for next iteration
           reader_done.store(false);
@@ -956,6 +941,20 @@ namespace skch
 
         mappingBoundarySanityCheck(input, output->results);
 
+        // Apply pre-filtering immediately after mapping against this subset
+        if (param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE) {
+            MappingResultsVector_t filteredMappings;
+            filterByGroup(output->results, filteredMappings, param.numMappingsForSegment - 1, false, *idManager, input->progress);
+            output->results = std::move(filteredMappings);
+            
+            // Also apply length and identity filters
+            filterWeakMappings(output->results, std::floor(param.block_length / param.segLength));
+            if (param.filterLengthMismatches) {
+                filterFalseHighIdentity(output->results);
+            }
+            sparsifyMappings(output->results);
+        }
+
         return output;
       }