a simple thing that i always do not only on my pen drive but all my hdd partitions as well.....do this please, it will save a lot of hassles
make a file / folder named autorun.inf
then do the steps below
01) open my computer
02) tools > folder options
03) Click on the view tab
04) Uncheck the last option in the list "Use simple file sharing"
05) Ok > Close main window
06) Go back to the file / folder you created.
07) Right click > Properties > Security tab > Click Advanced
08) In the permissions tab , uncheck the option " Inherit from parent.......defined here"
09) Click on "Copy"
10) Apply > Ok
11) Back in the properties window , select each option from the "group or user name" section and click remove, one by one so that the window is now empty.
12) Apply > OK.
viola! any autorun virus can now not hit your hdd or your pen drive.
Alternatively
http://www.precisesecurity.com/tools-resources/adware-tools/flash-disinfector/ can also be used.