If your Pendrive is infected with Autorun.inf New folder.exe Iexplorer.vbs or any kind of Malicious Malware or Virus then you can remove it easily. Follow below Steps.
Actually this viruses are hidden and can’t be seen even after you enable show hidden folders.
Following simple dos command will change the attributes of these files ,there after you can remove it by pressing delete key.
Step1.: Type cmd in Run
Step2.: Switch to the drive on which pen drive is connected (like C:> h: enter)
Step3.: type exactly as attrib -s -h *.* /s /d and hit enter (don’t forget spaces).
Now you can see hidden virus files and you can delete them.