You "hide" things by managing Site, list/library, folder, item/page permissions.
In your example "level1" is a Site Collection. You delete these from Central Administration. "level2" could be either a subsite or a library. Site Owners and Site Collection Administrators can delete subsites. Site Owners can delete libraries. "level3.aspx" is a web page. It can either be deleted from the library named "level2" or from the root of the site using SharePoint Designer.
If you just want to hide content from search, there is an option in each site's Advanced Settings to exclude the site from search. Libraries have a similar option.