If you want to remove a site element (menu, frameset, business process, URL) from the site, thus making it unavailable for the users, you have to remove the site element from the site structure.
Use the menu item "Site structure -> Site Structure" to enter the site structure maintenance page.
Select the site element, you want to remove. Press "Remove".
This will lead you to a confirmation page, where you can either confirm or cancel the removal of the site element.
Please note that removing the site element does not delete the site element itself, it is only removed from the tree.
Removing a site element that has a child elements removes both the site element and all of the child elements from the tree.
However, the connection to the child elements is maintained. So if you at a later time add the site element to the site structure again - all of the child elements will be added as well.
You can't remove the site root.
Removing elements from the site structure can of course have significant impact on the way the users experience the site.
If you remove a menu item from a menu, a user who have already loaded the menu might experience an error when activating the menu item - when reloading the menu the user will experience that a menu item suddenly disappears. in other situations users might experience a change of content of a frame, when reloading a frameset.
You should of course consider the above, when updating the site. In some situations it is not a problem, in some situations you might wish to show a site unavailable page, when doing the update. Another option is to wait until a time, where the traffic on the site is minimal, to impact as few users as possible.
One special case, which needs special attention is the administration interface.
By removing either a top frameset or the top administration menu it will in fact be possible for an administrator to make the administration menu unavailable for himself. This will render the site impossible to control. Therefore it is strongly recommended to keep an instance of the administration interface open in a separate window, when making the changes.
Before closing this window you should reload the start page in another browser and check whether the start page is shown correctly - and that the administration menu is available.