If there is one virus lurking on your USB drive, you never know what might be propagating on your main system.Normally I’d make something this simple the first step.

Normally the file system that it already has will be the file system that is best suited for the drive. This gives you an overview of all drives connected to your system. The Format window contains several customizable options, such as the aforementioned File system, the Allocation unit size, the Volume Label, and the Quick Format option. As we are dealing with a potential hardware issue, uncheck the Quick Format box.

That will force the format to do more than just erase files.

Depending on your antivirus software, you may be able to configure it to automatically scan a USB drive when first plugged in.

If not, you can navigate to the USB drive in Windows Explorer, right-click, and force a manual antivirus scan.

If you do find a virus, eliminate it using your antivirus software.

At this point, I would advise performing a full system scan after updating your virus definitions.

Samba is a software suite that allows you to access file systems over the network.

From Retro Pie version 3.0 a file manager is available, it allows you to manually transfer files between USB-stick and Raspberry Pi SD card.

The only thing left to do is stick the files onto a USB flash drive.