If you mean the ends are sticking out past the fretboard as in sprout, I like this procedure I picked up a while back on youtube:
Put masking tape down the side of the fingerboard. Then slide your file or even just sandpaper over it. The sharp frets will star to stick through the masking tape and you can continue to sand until it is smooth. Even a fine 600 grit sandpaper can do a lot. I now have a fret file from CB Gitty for this work. It's about 220 grit I think...so great for fret sprout...but you have to work up to finer and then polish eventually. It's important to round over the ends too for even smoother playability. I also recommend browsing youtube, etc. for ideas. There are several ways of doing things and one method might appeal to you more than others. I usually end up using a combination of tips to form my own way of doing things.
I also have a couple of extra, proper fretting files, but find sandpaper can work just as well for some of the tasks...except for crowning..It'd be hard to crown a fret with just sandpaper.