So WHY do you want to lower the frets? Do you have a few high spots, or buzzes? Are you sure filing the frets is what you want to do?
Stewart Macdonald has a good book on this. Also it would turn out best if you had the right tools. One regular old garage file wont to the job nicely.
A quick but not instructional overview:
1. You use a long ruler with cutouts at each fret. This gets set against the wood of the fretboard as you re-set the truss rod nut to straighten the neck. Unlike a normal set up, this is done with no relief. You actually set it up dead straight.
2. You figure out what frets are high. Typically using some short chunk of straight metal to rock between any three frets. If it rocks, the middle fret is tall or the outer fret has a low spot.
Also smearing the frets with marking pen, and then swiping a sandpaper radius block down the neck will leave the low spots with ink.
3. When filing tall frets you need to keep them following the radius of the neck. Use the radius block and ink method to check between taking a few carefull swipes with a fret file. Or maybe even just use the radius block and sandpaper alone if the frets are close to the right height.
4. Now that the fret tops are flat, you need to round them again. A concave fret file exists for this. Really skilled old-timers can do it with a small triangular file, but mere mortals use a cupped fret file. Then you check for rocking frets again and maybe do some spot leveling if you removed too much material while rounding.
5. Polish the frets. All of this needs to be done with something guarding the easily marf-able fret board.
6. Cut deeper nut grooves if nessisary if frets were lowered significantly.
7. Re-string guitar, tune to pitch, adjust bridge height, adjust neck relief, intonate bridge, adjust saddle height again, check neck relief again, adjust intonation again, do it all again a few hundred times until it is close enough to give up.