I don't want you to mess it up further, BUT... what if you took a razor blade and trimmed it flat, took the shavings and stuffed them down into the holes, then threw a piece of parchment paper over the area and used the tip of a regular clothes iron to smooth it down? This might be worth trying as a test in an inconspicuous area first!
Otherwise, I'd trim it down with a razor blade, mix the shavings with epoxy and fill with that.