To remove visibility for a custom relationship you will either need to remove the custom relationship from the employee's profile or change the settings for the custom relationship.
Remove visibility into a Lattice tool entirely
Navigate to Admin > Organization > Directory.
Find the employee you would like to remove another employee's visibility into.
Click on the ellipsis (...) > View profile details to the right of that employee's name.
Under the Custom section, click the 'X' next to the employee's name to remove visibility.
Click Save.
Remove visibility into a specific Lattice tool
Navigate to Admin > Settings > People > Permissions > Custom relationships.
Within the custom field row, click Edit.
Next to the preferred tool, uncheck the permission box.
Click Save changes.