If your usb drive has directories with .exe extension and most of the directories are not even show, your disk is probably infected with the virus.
To fix the problem without a hassle, download Malwarebytes free anti virus program. It is one of the best, does not bloat your system, does it job really really well. It is recommend to first scan your main OS (quick version is fine). It will clean your system even if the virus is in the memory. Next once your OS is clean. Right click on the drive that is infected and choose Malwarebytes to scan the drive. It might take a while, upto an hour or more to go through the entire hard drive.
Here is my log file.
Scan type: Quick scan
Objects scanned: 178749
Time elapsed: 1 hour(s), 9 minute(s), 48 second(s)
The name of the virus was Malware.Packer