USBDriveFresher is a free software tool for Windows which can automatically remove those unnecessary junk files from the USB drive when you connect it to your computer.
Using this tool is simple. It is designed to be a "Set it and forget" tool. Download and install it. Default settings are enough for an automatic clean up, you only need to run the tool once otherwise you can enable the option ‘Run at Windows startup’.
Expert users can define a clean up rule. You can add file extensions that you don’t want on your pen drive.
USBDriveFresher absolutely free and runs under Windows 2000/XP and Vista. Download the tool from here.