Polyfill is better than foam. The foam in a sub enclosure is rather pointless. The wavelengths involved are so long that standing waves in the enclosure aren't an issue. Home cabinets benefit from the foam because you're usually allowing the woofer to play up into the midrange. Not so with a car sub.
For the OP, I have painted my last two MDF boxes with very good results. Round over the edges. Sand it all smooth, blend the seams, etc... Spray it with high build automotive primer, heavy on the end grain so it fills the end grain with primer and can be sanded smooth. For the first box (pics in my gallery) I sprayed it with SEM texture spray followed by satin black. On my newest box, I sprayed it with Rust O Leum hammer finish black with some trim pieces done in hammered silver. The result was really nice.