By default, Thunderbird shows the namespaces of IMAP folders as a seperate folder containing the subfolders belonging to that namespace. An example of this is when you use Google Mail and have IMAP access configured.
An add-on exists for Thunderbird which gets rid of the namespace folder and sorts all subfolders in the root tree:
This is particularly useful for Google Mail where the sent mail, trash and other system folders are stored in a namespace called [GMail]. This way, these folders are stored directly in the root of the tree rather than in a subfolder named after the namespace.