Hi Linda,
If you only need to clean up the hole, not the uh ... whole ... bead, then I suggest a
bead reamer (manual if you need just a tiny bit of cleanup around the hole, battery operated if you want to enlarge the whole hole).
Whenever filing or drilling resin, hold the item underwater to prevent breathing the fine particles. Drilling underwater also prevents overheating, which might discolor your resin or items embedded in the resin.
If that doesn't answer your question, let me know in more detail which part(s) you want to file for which reasons, and I'll get a better answer for you. I don't personally use resin, but I have an experienced pool of people to ask!