To terminate an account in WHM :
From the Accounts Functions section in the left-hand sidebar click 'Terminate Account'
The following page will show you two boxes: one that lists all the current domains and one that lists all the current users.
If you want to remove a domain entirely select it from the box on the left and click the Terminate button
If you only want to remove a user account select an account from the box on the right and click the Terminate button
Once you have performed either one of these you will be taken to a page telling you the account has been terminated.