You can create a folder structure in the 'Files' section of a workspace. Simply click on the 'New' button and select 'Folder' from the drop down menu.
It will then create a folder in the current position. Click on the folder's name to enter the folder and upload files into it. You can create as many layers of sub-folders as required.
If you select folders by clicking on one or more of their check boxes, a 'Select action' button appears with drop down menu of additional functions.
If you want to move a files/folders simply select the 'Move' option from the list and you'll be presented with a list of workspaces (and the folders within them) - just select the Workspace (and sub folder if required) and then press 'Move files'.