I think I found a good solution for this. Especially because I plan to keep 2 different ROM libraries.
1. Is my filtered out library of games I intend to play
2. Is the full mame set, in case I ever want to add something back into the library.
Lightspeed seems like it'll work out well. What I'll do first is filter the full mame set, but very broad. I'll take out obvious stuff I have no use for (Such as casino games), and then I'll run through the list of games it gives me, removing anything I don't want.
When I'm ready to go, I'll choose the option to copy/move the roms into my filtered folder. This way I can keep the full set as a backup, and all the games I do want will go into the filtered library.
I'll report back!