FR4 is fibreglass, and it is hazardous to inhale the dust. Be sure to wear goggles, gloves, a protective mask (not a medical one) and work in a special area that you don't live in. Collect all dust by doing it on top of paper or plastic that you fold together and get rid of. Then change clothes.
I also use a vacuum cleaner nozzle propped up to point directly at the item I'm working on. That way, the vacuum should suck up most of the dust.
As to tools: Dremel with cutting wheel or routing bits.
