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There's two ways how you can download your uploaded files from your submissions?
Method 1: Using the File Downloader app. You can check it here: http://apps.jotform.com/app/file_downloader.
Method 2: Using a Mozilla Firefox extension to download all the uploaded files. We have a guide it here: http://www.jotform.com/help/315-Downloading-File-Uploads-in-the-form-using-DownThemAll-Mozilla-Firefox-Extension.
I would advise using method 2 because this is less technical to setup, but you can both try both methods.
Let us know if you need further assistance on this.