The assumption within your question is that you are dealing with sprouted fret ends due to a dry neck and low humidity, not shaping the frets ends during a re-fret or the initial installation. Perhaps I have misinterpreted.
I do it by hand with a standard medium-fine mill file about 12" long. Two layers of low-tack painter's masking tape to protect the finish at the neck joint, maintain roughly a 60° vertical angle from the fret plane, and go slowly and smoothly along the length of the neck with light pressure. You only want to remove the high points of exposed metal, not take off any wood from the fret board edges or binding. I also do this before re-humidifying when the neck wood is at its narrowest, and generally never have to do it again on the same instrument.
Disclaimer: I am not a professional luthier or repair tech, nor do I play one on TV. I'm just a handy guy with some mechanical skills that only works on my own instruments or a few for my students who won't / can't pay for a shop repair, and stay well within my skill level and comfort zone.
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