Give the fin box a sand with fine wet and dry, get the hose out and go for it. This will get some of the black paint and any imperfections out of the fin box.
Buy a file.
Test fit and calculate amount and location of fin mod.
Begin modification with file, clean up with one of those sanding blocks, test fit, repeat till perfect.
BTW Is this a Makani fin ?, I had a a couple of where I spent over an hour getting the fin to fit

, still good fins though