And somewhere there is a guide to remove them all.
You cannot just delete them. They have to be removed a few at a time from ships, mdlnames, descript.dat, and I think Objects_dp.....
Seems to me you can only remove about 10-12 at a time, open CFS2, shut down, delete filelist.dat, *.cdp, INDEX and remove 10-12 more; REPEAT until they are all removed.