Kinda confuse. I have a pop account from my ISP. I received my mail via apple mail. Then I login in to my webmail account from my ISP and it is still all there. The only way is delete the emails from webmail or command I from the inbox. Shouldn't it automatically be remove from server? I have trying searching but coming back with too many hits.
Go to Mail->Accounts->Advanced Look for the checkbox "Remove copy from server after retrieving a message:" Make sure the checkbox is checked then in the pull down option below select "Right Away"