How to clear up stained white dog hair.

My dog is older and has some warts that he sometimes scratches and they need cleaning. After I use the medication, which is a dilute solution of tea tree oil I get at an herb store, it seems to clear the infection, but leaves a brown stain on his white hair.
I asked the Vet what might work and he said to try peroxide. He fooled around a little bit with trying it at the office, but it didn't seem to work well.
There has to be something that works. Even when he doesn't have a open sore, he looks awful because of the brown on his hair.
It isn't from licking as the spots are on his back and upper shoulder where I know he can't be licking, but that is what they look like.
The vet says that the warts are harmless and to remove them would be for cosmetic reasons. I have had them removed in the past and more just appear as he is just prone to getting them. I want to limit surgeries on him since he is a senior dog of 15 years now.
I was surprised to see some of them shrink down to almost nothing after using the Tea tree solution I heard about in Whole Dog Journal. I just love that magazine.