Format your Pen-Drive using Drive manager

If there is big virus in pen drive in that Prevents drive from formatting then try the following Steps

1. Right click on my computer

2 Then click on manage

3 Disk Management

Here u see all u drives . right click on pen dirve an format

OR

To prevent a pen drive from infecting of  Trojans or some kind of virus which uses autorun.inf file to execute, just create a blank folder in your pen drive and name it as autorun.inf make it hidden and read only. This trick is sometimes helpful to prevent those kind of viruses or Trojans.