Use your AV to scan the USB drive, look for the name of the Virus/Trojan
Download a fix for the particular virus/trojan, should be less than 50kb.
If this does not work, create a folder in a blank pen drive called autorun.inf. Then hide and write protect this folder. Also create recycle.bin... this should take care of most viruses or trojans. Then copy your data.
If all these fail, try clamwin, but you need to install updates for clamwin to work. Portable version runs off the USB drive, so you can use to to clean the host computer.
