I say Sand-Away. If you screw it up, replacements aren't expensive. I used a belt sander on mine. Took off a lot. The one problem was I didn't keep the correct angle so it wasn't linear across the strings, more off the high E than the low E. I eventually took mine in to a luthier to have done properly. He did everything; frets, neck, saddle and something else I don't remember. It plays nice, but not as nice as my piece o' junk Ovation. That thing plays like an electric.
I think the main thing you have to be cautious of is to ensure there is still an angle between the saddle and the pins.
I know Mutt is going to correct me on something.