then it will be hard to get it out. you need to get to the stain and basically remove the stained layer of the tube material.
the harder the tube, the less is staining. For example glass tubes (mayhem and alphacool make them) are stain free. They also don't get "clouded" over time.
so easiest would be just get a new tube to replace the stained. Try to avoid cheap tubes as the release some staff into liquid that can clog the loop. Primochill are known for quality flex tubes.