I do have a sanding block with different grits on different sides, would this be okay to use over the top of the nut?
It sort of depends on what grits are on your block. A flat file is better to remove most of the material first, then do final shaping and polishing with sandpaper like Simon described. That said, if all you have is sandpaper, you can do it. It will probably just a take a bit longer.