You could try an small piece of cloth with some metal polish if it is bothering you. Just be careful not to get any on the base. Even a small amount of steel wool or a simple scouring pad. Again try not to damage the base.
Personally, I would take the board into your local snowboard shop and ask them. They may have an alternative. Even though it is a new board, you could ask for a tune up, the simple process of waxing the base may cover the scratches and the tuning would remove the surface rust.