A: Organizational permissions are always inherited in organization tree which gives user read/write permissions to the user to selected department and all sub-departments.
It is not possible to add exception to a specific departments within the organization to hide it from the user.
However there is alternative way to hide departments from users with organizational permissions and additional level in the department tree.
If you have already built your organization tree and assigned user permissions to users you may have to re-structure the tree and assign permissions once again to all existing users.
You have organization tree as below and users have access to entire organization.
Permissions are inherited from top department (Intersolia) to all sub-departments.
You can create one additional level between the "top" department and its current sub-departments which will then work as a new top for the users.
When department is created the previously created departments should be moved to the new department.
After this you can add new branches in the tree below the actual top department which only permitted users should be able to find.
In this case if user should have access to entire organization (including the hidden departments) you can assign permissions to the real top department (Intersolia). User will then inherit permissions all departments.
If user should only see the previously created departments you can assign permissions to the newly created department. (Department)