Puberty. Needing to look a certain way... Oh memories...
You can get warts frozen off at the doctor's office. The home-remedy wart freezing off kits are very ineffective. They just don't have the same power that the ones the doctor's use have. You can do lazer removal, but it leaves an ugly scar. Essentially you just have to keep taking your kid in and having the warts re-frozen until they are gone.
Deeper than this though is that our children will have to decide if their happiness is going to be held hostage by a wart or not. If it isn't a wart, it will be a pimple. If it isn't a pimple, it will be their brand of jeans not being right.
One of the greatest examples of good self-worth I ever met was this little old man in Japan who wasn't much taller than a child. He was covered from head to toe in warts and right beside him was the most devoted, sweet wife I had ever seen. Instead of looking for wart removal systems that worked, he did personality development and ended up having a great life filled with dignity. Dignity that he encouraged others find and stand as a pillar for.
Maybe talk to your son about whether he believes people should be liked for what they look like or for who they are. Maybe his wart can become a symbol to him for standing up for each and every person's value. At least it can offer him some good practice in standing up for everyone's personal worth and something to do until the wart eventually goes away =). Warts...great leadership training in disguise!