You'll need a way to access your server files. This tutorial references our panel, but you can also use SFTP. Shutdown your server before proceeding!
Either way, go to the root directory of your server. On the web panel, this can be done by selecting your server, dropping the "Server Management" menu, then selecting "File Manager". When you connect to your server via SFTP, you should be already at your root directory.
CAUTION
The following steps will completely erase your worlds. If you wish to have multiple worlds on your server at once, add a prefix to the end of each world (such as _old), OR use a plugin such as Multiverse. We recommend you take a backup before deleting any worlds in your server. Follow this guide to learn how to make and schedule backups.
You now have to locate your world files, on most Minecraft servers these folders will be world, world_nether, and world_the_end - if not, check your level-name in server.properties.
Select the world(s) you want to delete with the checkboxes on the side, then drop the "Mass Actions" menu and select "Delete Files" - then confirm the deletion. Deleting these files should only take a few seconds at most.
Then, go ahead and start back up your server. This will take longer than usual as it generates the spawn area.