The overall category hierarchy can be managed by editing category settings. Categories can also be hidden from view as can individual courses, although they can still be seen by administrator level users. Normal users are unable to see the hidden category itself and are unable to see any subcategories or courses that are in the hidden category.
Moodle has a course and category management page to enable easily:
creation of new courses and categories
changing the order in which courses and categories appear on the page
moving courses and categories into other categories
editing, hiding, and deleting of courses and categories
You can access this page through the administration block via Site administration | Courses | Manage courses and categories:
