When I was little, I had a bunch of figures, but no portal or game (I just wanted to collect them) and I colored the bottom the base with a sharpie. Will they be able to be used still? Can I clean it?

Coloring them with a Sharpie pen won't hurt their functionality on the game portal, so they should still work with the games just fine. As for cleaning off Sharpie, try using a dry erase marker, repeatedly marking over the sharpie area, and wiping off with a towel or similar cloth. However, after a few times of trying this method, it will wreck the dry erase marker, so be ready for that.