You'll need to configure this per mail account. Head here:
Tools > Account Settings > [account] > Server Settings
In the Server Settings section that comes up, you'll see an option to delete from the server:
- Leave messages on server
- For at most [x] days
- Until I delete them
Chances are you've got the Leave messages on server option checked. Uncheck that.
If instead you want them on the remote server for a certain period before delete, check the box and then set the number of days you want in the For at most [_] days option.
Next time Thunderbird downloads your mail it will delete them from the mail server and leave the only copy being on your local machine.
If you've set up your account in version 3 using the wizard it would have defaulted your account to IMAP settings. The above instructions won't work unless you recreate that account under POP settings.
To do so set it up again and transfer your mail across:
Tools > Account Settings > Account Actions > Add Mail Account
- Fill in the details for Mail Account Setup
- Click Continue
- Click Stop to halt the wizard
- Click Edit
- Change the Incoming from IMAP to POP
- Click Manual Setup
You'll now see the options first mentioned under the Account Server Settings