Pure eucalyptus oil works excellent, won't damage your minifigs, (and it smells good too!). You can get it in small bottles at health-food stores, pharmacies, and Asian stores. You don't need much, so a small bottle can last you a long time.
Just pour a little of the oil on a piece of cotton or soft towel, and rub over the printed area you want to remove. It gets wiped off almost right away. If it is a small area you want to remove, use a Q-tip. Just be careful not to touch areas you want to leave intact as the oil works pretty fast. Wash off the minifigs with pure water afterwards.
You can also use Brasso (the metal polish), but it takes a bit more rubbing and it smells really bad. But it does a good job in general and won't damage your minifig. It is also easier to control than the oil on small surfaces as it is more like a paste and won't run like the oil could. Make sure you rinse the minifigs off really well once you are done.