You can hide the "Folder selection" option on the upload files page as follows -
- Navigate to the About Drag, Drop & Upload to Amazon S3 tab.
- Scroll down to Step-6 of Important Post Install Steps and turn on the toggle of Hide Folder Selection and click Save as shown in the image below-

PS: View Drag, Drop & Upload Files to Amazon S3, a Salesforce AppExchange app for moving files from Salesforce to Amazon S3: https://appexchange.salesforce.com/appxListingDetail?listingId=a0N3000000B5ZPqEAN