diff --git a/ROMFS/CMakeLists.txt b/ROMFS/CMakeLists.txt
index 3fd879e032..3229d3142f 100644
--- a/ROMFS/CMakeLists.txt
+++ b/ROMFS/CMakeLists.txt
@@ -84,6 +84,9 @@ add_custom_command(OUTPUT ${romfs_gen_root_dir}/init.d/rcS ${romfs_gen_root_dir}
 	COMMAND ${CMAKE_COMMAND} -E copy_directory ${romfs_src_dir} ${romfs_gen_root_dir}
 	COMMAND ${CMAKE_COMMAND} -E remove_directory ${romfs_gen_root_dir}/init.d-posix
 	COMMAND ${CMAKE_COMMAND} -E remove_directory ${romfs_gen_root_dir}/mixers-sitl
+	COMMAND ${CMAKE_COMMAND} -E remove ${romfs_gen_root_dir}/mixers/CMakeLists.txt
+	COMMAND ${CMAKE_COMMAND} -E remove ${romfs_gen_root_dir}/init.d/CMakeLists.txt
+	COMMAND ${CMAKE_COMMAND} -E remove ${romfs_gen_root_dir}/init.d/airframes/CMakeLists.txt
 	COMMAND ${PYTHON_EXECUTABLE} ${PX4_SOURCE_DIR}/Tools/px_process_airframes.py
 		--airframes-path ${romfs_gen_root_dir}/init.d
 		--start-script ${romfs_gen_root_dir}/init.d/rc.autostart