No Windchill or other PLM system, so that makes this very simple.
Open your top most assembly and its drawing, if you have one.
Create a new folder in Windows for your now finished files.
Do A File-Save As-Backup to that new folder of your top level file.
All of the files used in that file will now be saved to the new clean folder.
I would hold on to the original folder for a few days to be sure everything loads properly.
If you use search paths, change them to your new folder and remove the old folder from the search list.