My answer to this from what I've found over the years is that you have far more control with a file than you do with any cutter - I always leave some sprue on the part and file it back, rather than try to cut it flush with the part. That way if I slip with a blade the waste sprue gets the damage, not the part.
BTW - you can do this with a razor blade, nail cutter, etc. It's just a matter of how close you cut to the part.