I scratch my intake manifold a little not bad just a little scratch and there gasket material left over that I can't scrap of with any plastic. Should I use sand paper to remove the remains material and smooth out the surface?
Did you try a metal gasket scraper tool? What about a wire brush on an electric drill (asking, don't know if that's OK)?
If a scraper doesn't work, use a flat fine tooth file, and lightly run it across the machined surface, making sure to keep it flat.
NEVER use a wire brush, especially a powered one, on a machined aluminum surface! You're right to be cautious with that suggestion Cusser.
What about a brass brush?
Both types of brass that I know of are harder than cast aluminum. If you want to gamble, It's your stuff.