Yeah there's really not an easy fix for this. I spent days cleaning (culling) my Roms for this issue. Clrmamepro can give you lists that you can then make batch delete files with (or move). Romlister is I believe what I used, as I was able to make plain text lists including removal of roms like trackball, hanafuda, quiz... Another trick if you have on your computer the emulators, is to go through their favorites, fighting, 4 button.....lists, and make those batch files that move or delete the roms (ask the Google how its not hard).
It should go without saying that you use a split set if you didn't already know, otherwise you can't remove the individual builds from the roms. In case you were unaware. Good luck, it just takes some tlc.
