How big are the spots?
If they are small, the most likely diagnosis is one of the two organisms that can cause black ich.
I believe that the preferred treatment, regardless of which organism you have, is formalin baths.
Check out the FAQ sticky at the top of this forum. There is a section about how to do formalin baths.
Be careful with the medication as it can be toxic to humans.
There is also a picture of black ich in the diseased fish sticky that your should check out.