Fist you will need  to hide the Users department(s) from the front-end that you do not want to be searchable

To do this navigate to:
  1. Academics
  2. Scheduling
  3. Requests and Schedules
  4. Departments and Courses 
  5. Click the Editing Pencil next to the Department you are looking to remove from the Public Directory
  6. De select the Publish to Front End checkbox
  7. Click Save and Close

Now navigate to:
  1. Core
  2. People Finder
  3. Search for user
  4. Access tab
  5. Click Employment 
  6. Click Edit
  7. Remove the grade levels associated with the User

If you still want the user to be searchable in the Directory behind the password then you would need to create another department to associate the user with that is not published to the front end (using the first set of steps above) this way the User can still be found attached to a department otherwise if you do not associate them with another department they will not display on the secure Directory.