You can delete the add-on domains and sub-domains from the cPanel. Please refer to the below steps for the same.
How to remove Addon Domain in cPanel?
1. Log in to the cPanel account.
2. Go to the Addon Domains.
3. Under the Modify Add-on Domains, You can remove the Domain. Click on the Remove Button.
4. You will be asked for confirmation to remove the Add-on domains. Click on Remove. 
How to remove Subdomain in cPanel?
Similarly, you can remove the Subdomain as well.
1. Go to the Subdomains from the Domains Section. 
2. Click the Remove Button for the subdomain you want to remove. 
3. It will ask you to delete it permanently. Click On Delete Subdomain.
Note:
- You can not delete the Main Domain from your cPanel account. If you want to change the Main Domain, please get in touch with our Support Team.
- Deleting the domain will remove the domains/subdomains only. The web files/data will not be removed by the system. You can remove the data from the File Manager.
