For anatomy, there's just no getting around rote memorization. One of the best study aids that I have used to memorize thousands of names has been flash cards.
While studying Japanese, flash cards were incredibly useful. I would cut paper into small strips that were easily handled and create thousands of flash cards. I still have a box with every card that I've ever made. On the front, I'd write the kanji with the accompanying furigana and on the back I'd write the meaning, plus a few example sentences in how to use the word. One drawback was that creating each card took an inordinate amount of time, but it was well worth it.
Anatomy poses a different challenge for using flash cards. Since anatomy is often a visual exercise, pictures of the target muscle, artery, nerve or other landmark need to be visualized. Drawing a picture for each name would be too infeasible.
In comes this nifty flash card program.
http://www.vendant.com/FlashCardManager/program.aspx
Not only can you write words, you can also include pictures. Practicing by looking at a picture, then naming all of its parts is a bit more effective than looking at a word and then trying to visualize a picture in your head. Eventually, with enough reviewing you should be able to visualize in reverse as well.
Creating your own cards takes time, but you should be able to master your creations soon enough.
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