go to Mail -> preferences ->accounts (choose your .mac) -> Advanced. You will see a checkbox that says "Remove copy from server after retrieving message". Beneath is a dropdown to set how long of a "lag" before they are removed from the server (mine is set for 1 week, the default, I believe). You should be able to press the Remove Now button beside that dropdown to clear them right away.
Best O' Luck
edit: hmmm, I just re-read you post and am not sure that I answered what you were asking. If all else fails, log in to your .mac account as webmail from your web browser. You should be able to clear them directly from the .mac webmail interface.
Whenever I delete the messages, the next time I synchronize with the server the deleted messages reappear. What the heck is going on here? After deleting the emails, I click "Erase deleted messages", I deleted the mail preferences, deleted the mail folder in my profile.
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