diff --git a/ROMFS/CMakeLists.txt b/ROMFS/CMakeLists.txt
index 1a4719e138..a8b6f99538 100644
--- a/ROMFS/CMakeLists.txt
+++ b/ROMFS/CMakeLists.txt
@@ -75,7 +75,10 @@ get_property(romfs_cmake_files GLOBAL PROPERTY PX4_ROMFS_CMAKE_FILES)
 get_property(romfs_copy_files GLOBAL PROPERTY PX4_ROMFS_FILES)
 add_custom_command(OUTPUT ${romfs_gen_root_dir}/init.d/rcS ${romfs_gen_root_dir}/init.d/rc.autostart
 	COMMAND ${CMAKE_COMMAND} -E remove_directory ${romfs_gen_root_dir}
+	# TODO: we should only copy the files in ${romfs_copy_files}
 	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 ${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