It is not obvious how to delete all files (including sub-folders) if you read AWS CLI S3 documentation. But there is a trick by using AWS S3 sync command
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cd ANY_EMPTY_FOLDER_ON_YOU_COMPUTER
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aws s3 sync . s3://YOUR-BUCKET-NAME --delete
Be careful! This effectively will empty your AWS S3 Bucket completely. You can do the same for nested folders.