You can sand the area flatly lightly and randomly with 80 grit, just before you get to the mdf, sand the whole panel with 400 grit This time flat, random and fairly aggressive (cross hatch type patterns over large areas work best) , Now if your hole is down to the wood and still a problem, wipe some glaze putty across it with a razor blade, (glaze is like bondo, but more for final finish trouble/pinholes ) .... Sand lightly, prime and refinish.