I found this tut on cleaning ur usb drives  manually very helpful and it shows all  those hidden batch file running  everytime u plug in ur usb flash drives

                         One of the ways by which a virus can infect your PC (http://javascript%3cb%3e%3c/b%3E:void%280%29) is through USB/Pen drives. Common viruses  such as ’Ravmon’ , ‘New Folder.exe’, ‘Orkut is banned’ etc are spreading  through USB drives. Most anti virus programs (http://javascript%3cb%3e%3c/b%3E:void%280%29) are unable to detect them and  even if they do, in most cases they are unable to delete the file, only  quarantine it. Here are the things which you can do if you want to  remove such viruses from your USB drives (http://javascript%3cb%3e%3c/b%3E:void%280%29)
 
 
Whenever you plug a USB drive in your system, a window will appear  similar to the one shown below
  (http://www.whoismadhur.com/wp-content/uploads/2008/01/usb.jpg)
 Don’t click on Ok , just choose ‘Cancel’. Open the Command Prompt (http://javascript%3cb%3e%3c/b%3E:void%280%29) by typing ‘cmd‘ in the run  box. In the command prompt type the drive letter: and  press enter . Now type dir /w/a and press enter.
 This will display a list of the files in the pen drive. Check whether  the following files are there or not

• Autorun.inf
  
• Ravmon.exe
  
• New Folder.exe
  
• svchost.exe
  
• Heap41a
  
• or any other exe file which may be suspicious.
  

If any of the above files are there, then probably the USB drive is  infected. In command prompt type attrib -r -a -s -h *.*  and press enter. This will remove the Read Only, Archive, System and  hidden file attribute from all the files. Now just delete the files  using the command del filename. example del  Ravmon.exe. Delete all the files (http://javascript%3cb%3e%3c/b%3E:void%280%29) that are suspicious. To be on a safer side,  just scan the USB drive with an anti virus program to check whether it  is free of virus or not. Now remove the drive and plug it again. In most  of the cases, the real culprit turns out to be the “Autorun.inf”  file which mostly gets executed when someone clicks Ok in the dialog  window which appears above. Thus the infections can spread
 
Security Tip:
 
Disable the Autoplay feature of USB drives. If you disable the  Autoplay feature of USB drives, then there are lesser chances of the  virus spreading. A tool which can perform such a function is Tweak UI (http://www.microsoft.com/windowsxp/downloads/powertoys/xppowertoys.mspx). Download it from here (http://www.download.com/Tweak-UI/3000-2341_4-10002117.html) install it.
  (http://www.whoismadhur.com/wp-content/uploads/2008/01/tweak-ui.png)
 Run the program. Now you can disable the Autoplay feature of the  removable drives as shown above. By following the above steps, you can  keep your USB drives clean. If there are any other methods which you  use, then share it with me through comments.