It depends on exactly what the problem is.
First check if frets are properly seated (if they raise up a bit from the wood they're super sharp). If no, then they need to be clamped (and maybe glued) down. Doing this might solve 'frets sticking out' problems.
Next check if the fretboard is dehydrated and has shrunken (fret ends properly seated but poking over the edge of the fretboard). If this is the case, it's probably not a bad idea to file/sand the frets down a bit but you will want to condition the fretboard with some mineral oil afterwards so that it expands back and the frets stop sticking out.
If the frets themselves are rough feeling, then it's a judgement call. You might want to slightly round off the fret ends with a file, or you might be able to get away with just using some sandpaper to smooth them out. I usually start out with 150 grit, then move to 200, 250, 300, 400, 600, and finally 800. If you take a thin strip of sandpaper and glue them to popsicle sticks they work pretty well for doing this sort of fine work and you can set the sandpaper just a little bit back from the edge of the popsicle stick so it's less likely to scrape the fretboard.
For any fretwork it's probably a good idea to use masking tape to cover the fretboard because you'll occasionally slip with your tools. There are metal fretboard guards that you can buy which are probably less fiddly and better than working with masking tape, but I've never used them. Also remember that you usually only want to take off a VERY TINY BIT of the fret when working. It's easy to overdo things and make 'em worse (especially with a file). The work itself is very simple, but it can be time consuming.