During the looping, while getting the file from the remote server, you can always take advantage of the Remote FileList variable attribute (path) which will contain the full path and name of the file on the REMOTE server. Use that to define the LOCAL path (in the Workspace maybe?) and write the file into the corresponding path locally. Then, you could read the workspace (recursively) and get a local fileList variable containing the same structure as the remote server.
Lead Solutions Consultant