No easy way to do this that I know of.
I did mine a little bit at a time. Opened MAME in Windowed mode, alongside an explorer window inside the roms directory. Gradually went through the alphabet, deleting chunks at a time, till I ended up with what I wanted to keep. I still have many versions of the same game (Think SF2 versions) because I OCD over MAME Dev changing up parents/clones etc.
With CLRMAME, I guess you could load the datfile and go through its list, unchecking what you don't want, then running a scan making sure "uneeded" is checked. Make sure you have a backup of your sets as its very easy to wreck your collection with CLR.
You might be able to find a datfile for CLR that will allow you to easily wipe the unwanted categories from your collection.