To empty a user's 'Inbox' folder, go to the VPOP3 settings. Then click on the Users tab at the top to go to the user list. In the user's list there will be a column displaying the number of messages in the user's Inbox folder. Just to the right of that will be an icon of a waste bin. If you click on that, you will delete all the messages in the user's Inbox folder.

In versions of VPOP3 prior to v5 this action may take a long time if there is a large number of messages in the user's mailbox. VPOP3 may appear to be not responding, but it will be deleting the messages, so you need to wait. In version 5 the action should be almost instantaneous.