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like in the movie Planes Trains and Automobiles, you should be able to buff that out no problem.
Just take enough away that it does't have any hard edges, so your blade can smoothly travel over it...

If it is a flap you can glue it down with rubber cement. If you can find some pumice it will work to smooth is off. It kind of depends on how bad it is. You might be able to use 600 grit to smooth...