Sure, it may sit in the depths of HR until the end of time, but you can be sure of two things: One, your former boss (and future reference) will read it and be impressed. And two, if you ever decide to come back to your company (hey, it happens), it's a very good thing that last thing on file is a great, professionally written resignation letter.
Also think about your relationship with your manager. Would he or she have reason to think that you'll waste your last two weeks or distract your co_workers instead of doing what you can to make the transition seamless? If so, you may be asked to cut your two weeks short.