Not the same. If you spilled milk on a chair, then you could refer to the chair and clean it, or refer to the milk and clean it up. You "clean" things that will be there when you are done, and you "clean up" mess that will be gone when you are done. It's the same as when you "use up" the milk. It's gone. It has all been used.

"Clean it up" is a phrasal verb meaning to make someone or something clean or neat. The meaning is the same :)