I love fun threads like these lol. my take:
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they are etched into his skin. not
actual whiskers although they do look like it. basically, imagine a pen that once you draw something on your skin, it'll dent the skin. (or for the morbid members imagine you using a knife to cut three lines on your cheek skin very deeply, and you get Naruto.)
orochimaru couldn't make them go away I believe. if he does manages to pop the skin surrounding his whiskers to appear normal, watch when Naruto enters Kyuubi mode because of ramen or sasuke, the whiskers will expand and it'll be much wider than before. thus making newer marks on his whiskerless skin
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then, once he turns back to normal the whiskers will be gone. :kakashi: