After doing what Kevin suggested, I would get the fenders sandblasted to bare metal and paint with epoxy primer before applying filler.
We found that most of the rust was in the flange where fenders bolts to the box sides. The rusted out areas had to be patched. I made a plywood template using the holes in the box sides as a guide. Bolted the fender to the template to make sure that the fender didn't get out of shape as I was working on it. Used the same template for both sides.
