diff --git a/CMakeLists.txt b/CMakeLists.txt
index 40102d99..0b09d292 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -76,7 +76,7 @@ protobuf_generate(
 
 #_____________________________________________________________________________________________
 
-set(PROTOBUF_PYTHON_GENERATED "${CMAKE_CURRENT_LIST_DIR}/build/python_kpex_protobuf")
+set(PROTOBUF_PYTHON_GENERATED "${CMAKE_CURRENT_LIST_DIR}/build/python/klayout_pex_protobuf")
 file(MAKE_DIRECTORY "${PROTOBUF_PYTHON_GENERATED}")
 
 protobuf_generate(
diff --git a/klayout_pex/fastcap/__init__.py b/klayout_pex/fastcap/__init__.py
new file mode 100644
index 00000000..73952843
--- /dev/null
+++ b/klayout_pex/fastcap/__init__.py
@@ -0,0 +1,23 @@
+#
+# --------------------------------------------------------------------------------
+# SPDX-FileCopyrightText: 2024 Martin Jan Köhler and Harald Pretl
+# Johannes Kepler University, Institute for Integrated Circuits.
+#
+# This file is part of KPEX 
+# (see https://github.com/martinjankoehler/klayout-pex).
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# SPDX-License-Identifier: GPL-3.0-or-later
+# --------------------------------------------------------------------------------
+#
diff --git a/klayout_pex/fastcap/fastcap_runner.py b/klayout_pex/fastcap/fastcap_runner.py
index 870bbbd6..4c5c2b0f 100644
--- a/klayout_pex/fastcap/fastcap_runner.py
+++ b/klayout_pex/fastcap/fastcap_runner.py
@@ -28,7 +28,7 @@
 import os
 import subprocess
 
-from kpex.log import (
+from ..log import (
     debug,
     info,
     warning,
@@ -36,7 +36,7 @@
     rule,
     subproc,
 )
-from kpex.common.capacitance_matrix import CapacitanceMatrix
+from ..common.capacitance_matrix import CapacitanceMatrix
 
 
 def run_fastcap(exe_path: str,
diff --git a/klayout_pex/fastercap/fastercap_input_builder.py b/klayout_pex/fastercap/fastercap_input_builder.py
index c20bef6d..70cf51ef 100644
--- a/klayout_pex/fastercap/fastercap_input_builder.py
+++ b/klayout_pex/fastercap/fastercap_input_builder.py
@@ -46,7 +46,7 @@
 )
 from ..tech_info import TechInfo
 
-import process_stack_pb2
+import klayout_pex_protobuf.process_stack_pb2
 
 
 class FasterCapInputBuilder:
diff --git a/klayout_pex/fastercap/fastercap_model_generator.py b/klayout_pex/fastercap/fastercap_model_generator.py
index 902625d3..1a4da99e 100644
--- a/klayout_pex/fastercap/fastercap_model_generator.py
+++ b/klayout_pex/fastercap/fastercap_model_generator.py
@@ -71,7 +71,7 @@
 
 import klayout.db as kdb
 
-from kpex.log import (
+from ..log import (
     debug,
     info,
     warning,
diff --git a/klayout_pex/fastercap/fastercap_runner.py b/klayout_pex/fastercap/fastercap_runner.py
index 31f32855..1ff3d0e2 100644
--- a/klayout_pex/fastercap/fastercap_runner.py
+++ b/klayout_pex/fastercap/fastercap_runner.py
@@ -26,13 +26,13 @@
 import time
 from typing import *
 
-from kpex.log import (
+from ..log import (
     info,
     # warning,
     rule,
     subproc,
 )
-from kpex.common.capacitance_matrix import CapacitanceMatrix
+from ..common.capacitance_matrix import CapacitanceMatrix
 
 
 def run_fastercap(exe_path: str,
diff --git a/klayout_pex/klayout/lvs_runner.py b/klayout_pex/klayout/lvs_runner.py
index a2052ed7..ce9166b7 100644
--- a/klayout_pex/klayout/lvs_runner.py
+++ b/klayout_pex/klayout/lvs_runner.py
@@ -27,7 +27,7 @@
 import subprocess
 import time
 
-from kpex.log import (
+from ..log import (
     debug,
     info,
     warning,
diff --git a/klayout_pex/klayout/lvsdb_extractor.py b/klayout_pex/klayout/lvsdb_extractor.py
index 89282e22..e9b55182 100755
--- a/klayout_pex/klayout/lvsdb_extractor.py
+++ b/klayout_pex/klayout/lvsdb_extractor.py
@@ -30,7 +30,7 @@
 
 import klayout.db as kdb
 
-import tech_pb2
+import klayout_pex_protobuf.tech_pb2
 from ..log import (
     console,
     debug,
diff --git a/klayout_pex/klayout/netlist_csv.py b/klayout_pex/klayout/netlist_csv.py
index aee76cc9..e0a61b96 100644
--- a/klayout_pex/klayout/netlist_csv.py
+++ b/klayout_pex/klayout/netlist_csv.py
@@ -25,7 +25,7 @@
 
 import klayout.db as kdb
 
-from kpex.log import (
+from klayout_pex.log import (
     info,
 )
 
diff --git a/klayout_pex/klayout/netlist_expander.py b/klayout_pex/klayout/netlist_expander.py
index 4dc1996e..19625dd3 100644
--- a/klayout_pex/klayout/netlist_expander.py
+++ b/klayout_pex/klayout/netlist_expander.py
@@ -28,11 +28,11 @@
 
 import klayout.db as kdb
 
-from kpex.log import (
+from ..log import (
     info,
     warning,
 )
-from kpex.common.capacitance_matrix import CapacitanceMatrix
+from ..common.capacitance_matrix import CapacitanceMatrix
 
 
 class NetlistExpander:
diff --git a/klayout_pex/klayout/repair_rdb.py b/klayout_pex/klayout/repair_rdb.py
index 2e2fede7..1721e39e 100644
--- a/klayout_pex/klayout/repair_rdb.py
+++ b/klayout_pex/klayout/repair_rdb.py
@@ -30,7 +30,7 @@
 import xml.etree.ElementTree as ET
 
 import klayout.rdb as rdb
-from kpex.log import (
+from ..log import (
     LogLevel,
     set_log_level,
     register_additional_handler,
diff --git a/klayout_pex/magic/magic_runner.py b/klayout_pex/magic/magic_runner.py
index 4ba9afa1..708301c9 100644
--- a/klayout_pex/magic/magic_runner.py
+++ b/klayout_pex/magic/magic_runner.py
@@ -28,13 +28,13 @@
 import os
 import subprocess
 
-from kpex.log import (
+from ..log import (
     info,
     # warning,
     rule,
     subproc,
 )
-from kpex.version import __version__
+from ..version import __version__
 
 
 class MagicPEXMode(StrEnum):
diff --git a/klayout_pex/rcx25/extraction_results.py b/klayout_pex/rcx25/extraction_results.py
index 0ba6c660..f368b8cc 100644
--- a/klayout_pex/rcx25/extraction_results.py
+++ b/klayout_pex/rcx25/extraction_results.py
@@ -26,7 +26,7 @@
 from dataclasses import dataclass, field
 from typing import *
 
-import process_parasitics_pb2
+import klayout_pex_protobuf.process_parasitics_pb2
 
 
 NetName = str
diff --git a/klayout_pex/rcx25/extractor.py b/klayout_pex/rcx25/extractor.py
index 6c0a9c1a..193c5499 100644
--- a/klayout_pex/rcx25/extractor.py
+++ b/klayout_pex/rcx25/extractor.py
@@ -40,7 +40,7 @@
 )
 from ..tech_info import TechInfo
 from .extraction_results import *
-import process_stack_pb2
+import klayout_pex_protobuf.process_stack_pb2
 
 
 EdgeInterval = Tuple[float, float]
diff --git a/klayout_pex/tech_info.py b/klayout_pex/tech_info.py
index e92c216a..bc8a2b11 100644
--- a/klayout_pex/tech_info.py
+++ b/klayout_pex/tech_info.py
@@ -29,9 +29,9 @@
 import google.protobuf.json_format
 
 from .util.multiple_choice import MultipleChoicePattern
-import tech_pb2
-import process_stack_pb2
-import process_parasitics_pb2
+import klayout_pex_protobuf.tech_pb2
+import klayout_pex_protobuf.process_stack_pb2
+import klayout_pex_protobuf.process_parasitics_pb2
 
 class TechInfo:
     """Helper class for Protocol Buffer tech_pb2.Technology"""
diff --git a/klayout_pex_protobuf/NOTE_-_POETRY_WILL_AUGMENT_THIS_WITH_GENERATED_PROTOBUF_FILES.txt b/klayout_pex_protobuf/NOTE_-_POETRY_WILL_AUGMENT_THIS_WITH_GENERATED_PROTOBUF_FILES.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/klayout_pex_protobuf/__init__.py b/klayout_pex_protobuf/__init__.py
new file mode 100644
index 00000000..e3097fa4
--- /dev/null
+++ b/klayout_pex_protobuf/__init__.py
@@ -0,0 +1,34 @@
+#
+# --------------------------------------------------------------------------------
+# SPDX-FileCopyrightText: 2024 Martin Jan Köhler and Harald Pretl
+# Johannes Kepler University, Institute for Integrated Circuits.
+#
+# This file is part of KPEX 
+# (see https://github.com/martinjankoehler/klayout-pex).
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# SPDX-License-Identifier: GPL-3.0-or-later
+# --------------------------------------------------------------------------------
+#
+
+import os
+import sys
+
+# NOTE: generated protobuf files will import other protobuf python files as if they were on the top-level, 
+#       while we want to have them in package klayout_kpex_protobuf
+# FIXME: see also https://github.com/protocolbuffers/protobuf/issues/7061
+
+_path = os.path.dirname(os.path.realpath(__file__))
+if _path not in sys.path:
+	sys.path.append(_path)
diff --git a/kpex.sh b/kpex.sh
index 35564f46..c9d171fc 100755
--- a/kpex.sh
+++ b/kpex.sh
@@ -26,5 +26,4 @@
 DIR=$(dirname -- $(realpath ${BASH_SOURCE}))
 
 export PYTHONPATH=$DIR/:$DIR/build/python:${PYTHONPATH}
-# /usr/bin/env python3 $DIR/kpex/kpex_cli.py $*
 /usr/bin/env python3 -m kpex $*
diff --git a/pyproject.toml b/pyproject.toml
index e0db5ad6..875b15b6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,26 +25,29 @@ classifiers = [
 ]
 
 packages = [
-    { include = "kpex", to = "klayout_pex" },
+    { include = "klayout_pex" },
     { include = "pdk", to = "klayout_pex" },
-    { include = "process_stack_pb2.py", from = "build/python_kpex_protobuf/", to = "klayout_pex" },
-    { include = "process_parasitics_pb2.py", from = "build/python_kpex_protobuf/", to = "klayout_pex" },
-    { include = "tech_pb2.py", from = "build/python_kpex_protobuf/", to = "klayout_pex" },
+    { include = "process_stack_pb2.py", from = "build/python/klayout_pex_protobuf/", to = "klayout_pex_protobuf" },
+    { include = "process_parasitics_pb2.py", from = "build/python/klayout_pex_protobuf/", to = "klayout_pex_protobuf" },
+    { include = "tech_pb2.py", from = "build/python/klayout_pex_protobuf/", to = "klayout_pex_protobuf" },
+    { include = "__init__.py", from = "klayout_pex_protobuf/", to = "klayout_pex_protobuf" },
     { include = "build/sky130A_tech.pb.json", to = "klayout_pex" },
     { include = "build/ihp_sg13g2_tech.pb.json", to = "klayout_pex"  },
 ]
 include = [
     "kpex",
+    "klayout_pex_protobuf",
     "pdk/**/*",
-    "build/python_kpex_protobuf/*",
-    "build/*.json"
+    "build/python/klayout_pex_protobuf/*",
+    "build/*.json",
+    "klayout_pex_protobuf/__init__.py"
 ]
 
 [tool.poetry.urls]
 "Bug Tracker" = "https://github.com/martinjankoehler/klayout-pex/issues"
 
 [tool.poetry.scripts]
-kpex = 'kpex.__main__:main'
+kpex = 'klayout_pex.__main__:main'
 
 [tool.poetry.dependencies]
 python = "^3.12"