If you're wanting to start from scratch, resetting your server to factory settings is very easy. Just log into Multicraft select and stop your server then follow these steps:

1. Stop your server.
2. On the left hand side click "FTP File Access". Then login.
3. Click (at the the very top of your server directory) the "All" button. This will select ALL files on your server.
4. Press the "Delete" button. (This will delete ALL your files). 
5. Press "Submit" to confirm you wish to delete ALL your files.
6. Once the process complete, go back into Multicraft, and your server's main page.
7. Select the server type you want ('Default' is the Default Factory Setting) and start the server.