Just take a gummy or diamond stone and remove the burrs. Slide it across the base a few times and side a few times till it's smooth. Just file the side edge, shouldn't have to worry about your base edge bevel.
Cro 's right. You want to use diamond stone to polish. A file will take off too much metal and you'll end up needing base grinds and your sidewalls planed to keep it flat with the edge
I personally use different bevels on my boards so I use an SKS tool with the file to set the angle and then polish and sharpen with a set of diamond stones. The tool just helps to stay consistent. I use it so much that it's more than paid for itself.
and how does a gummy stone differ from a diamond stone
Gummy and Ceramic stones are used for egde polishing too, they also come in different coarseness from rough to ultra fine. It's my understanding that the daimond stones are finer, keep their consistency longer, and are designed to fit into file guides, whereas the gummy stones are done used by hand.
so I would use a file only if I wanted to tune the edges, i.e. changing the bevel angles?
so for removing minor nicks, a diamond stone would be better because its finer??
and one more stupid question, I can deburr both the side edges and the base edges without ruinging the bevel angles? the nicks come in both directions.
I change the bevel angles with the file. This usually only needs to be done once. Then I put the daimond stones in the file guide to remove the burrs with a 200 grit stone, then I put in a 400 grit stone to start the polish and finish it off with a 600 grit stone. The guide ensures you stay on the angle you set the bevel at.