Hmmm, how aggravated is the dog? It might be hard to go, but try to stop it from scratching ot scraping them, as that will just make things worse.
As to how to deal with them, either a vet could lance them off, or try dabbing them with a little bleach each day. I had a wart on my toe as a child, and each night we whiped it with a tissue and a little bleach and it soon shrunk and went away.