Departments is added when configuring users/extensions and then available to setup a department head.
If you want to delete a 'department', the department must not be linked to any extension or user name. You can add the new department and then select the department for the extensions and user names, there after it will allow you to delete the 'old' department.
If the department is still linked to either user name or extension it will display the following message top left hand side after clicking on APPLY:
"Update Successful. Some departments could not be deleted!"
When you pull reports it will list all the departments that is in the TNG database. Therefore you can see departments on the 'Selection Criteria' for a report even though no user/extension is linked to it. This is because an entry in the TNG database has a call record where the user/extension was still linked to the department.