Today I cut out the aft bottom fuse skin template from the manual, and marked out the areas a needing to be trimmed. I found that taping the template to the outside of the skin resulted in good placement, and some masking tape held it in place while I drew out the area to trim.
I used a variety of tools to make the cut, a handsaw, bandsaw, vixen file and small files like the one in the picture. I was happy with the way this turned out.