First, you will have to create a connection profile.

When you create the automated connection profile, go to Automated Transfer Settings >> File and Folder Filters >> Configure. On the Configure Filters dialog, check the option for Select folder to exclude and click on the Exclude Folders under the FTP server section. Select the folders from which you want to exclude from the transfer. Click OK to save the changes.

Whenever you start the automated transfer, the selected folders will be excluded from the transfer. The files will be downloaded only from the non-excluded folders.