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Nail polish remover is great for getting permanent marker off of stuff, so I'm sure it would work on regular pen ink.
 
I think nail polish remover also works pretty well on removing the plastic itself. Have you considered trying just a mild abrasive, like Brasso or auto rubbing compound? i can't imagine the ink sank anywhere beyond just the surface of the plastic, so it should be pretty easy to just polish off.
 
You can get some quite cool stick-on skins for the Shuffle, so as long as the buttons aren't too badly covered, that could be one solution.

I've always wanted to do this to mine: 😎

ips-ahirst-300.jpg

Flower Power and Blue Dalmatians to you. 😉 Let's hope that Apple never decides to go too far again.

The Mister Clean Magic Erasers work really well on a variety of things. I figured it would take the paint off a wall but it didn't do that.
 
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