Zeus had Papilloma Virus when he was a pup. Trust me, I was just as worried. I took him to three or four different vets to try to diagnose it and get rid of it. (he was banned from protection training once it was discovered) There were a couple of vets who said that they could operate on it to remove it but the price range for both was around $300. SHEESH way too much for a wart that was supposed to go away on its own. Another vet said that she could, essentially, pinch it off with tweezers of some kind. That way the top of the wart would be removed while leaving the base of it inside his lip. It was supposed to speed up the process of developing an immunity to it. She was only asking for $80 to do it. I went for it since I wanted to put him back into protection training as soon as possible.
Zeus went in and stayed for the night so that they could keep an eye on him. The warts were all removed (he had 3) and within a week, you couldn't even tell that he had ever had warts. Don't worry. If it is puppy warts, it will go away on its own. If there is no need to speed up the process, there's no point in spending money to get it removed.