Please edit your automated transfer profile. Under 'Select Files and Folders to Exclude' click 'Configure'. Now, check the 3 subfolders you wish to exclude. This will only transfer the files in the root. You may also be interested in reading about filtering. This is useful when you only need to transfer certain types of files. More information on configuring filtering is available at this link: https://www.deskshare.com/help/AFM/Filters.aspx