By closing an open document, you finish the current session of working on this document. Later you could open this document again to continue working on it.
To close the active document, click the button on the toolbar of Atlantis.
You can also close the active document by choosing the File | Close command, or by pressing the Ctrl+W keys.
To close all open documents, click the button on the toolbar of Atlantis, or choose the File | Close All command.