Reflect your WordPress Real Media Library structure into physical, avoid the mess that you see through your FTP. Organize media in physical folders.
Demo: https://codecanyon.net/item/wordpress-real-physical-media-physical-media-library-folders-seo-rewrites/23104206
Demo: https://codecanyon.net/item/wordpress-real-physical-media-physical-media-library-folders-seo-rewrites/23104206