Firstly, you shouldn't go around colouring dogs with pens. But now that you have done so, you can try using specially formulated shampoos to remove tough stains. Also if the blot is small, it might wear off.
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You can use an oil, such as evoo, then use dawn to remove the oil. here is a link from a webblog i read about it.
http://www.practical-pet-care.com/archive.php?2005081406550831
If you wash the dog at least two times a week, it should come off in some amount of time. The amount of time it should come off? well, there isn't a specific time!