Files are organized in the following hierarchy: 


Bucket (Name of bucket: by default set as organization Id)

↓ 

Folder (Name of folder: object name prefix - the name of the object)

↓  

Sub Folder (Name of subfolder: record id) 

↓ 

Uploaded Files (name if uploaded file with versioning)




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