Hi
As Jules53757 say you can do this manually with informations shown in P3dO InDepth Tree.
Right click a node to delete a file.
P3dO pro (not free) AwkPlugin has a more advanced tool:
You select a CR2 or directory or bunch of directories, it will collect all files belonging to the scene(s). With Awk It takes only seconds to clean (empty directories are deleted).
The only problem is to take care not to delete shared Geometires.
Awk Plugin scene manager may also be used to move Scenes to another Runtime.
Yarp

Yarp - author of P3DO Organizer for Poser