Permanent markers come in very handy for marking golf balls but removing the marks seems a bit challenging. The stains from these writing utensils are evident on many surfaces and there are several methods out there that people have tried to remove them. Some seem more successful than others, so if one doesn't work, there are other options readily available.
Moisten the stain with water first to make it easier to remove.
Vigorously rub the golf balls with a paper towel soaked with regular rubbing alcohol. This method has been used effectively on many surfaces. Be persistent with the rubbing.
Try toothpaste containing baking soda, fingernail polish remover, Windex, WD-40 or non-oily hairspray if the rubbing alcohol doesn't work. Make sure to use plenty of clean paper towels for this.