Using cmd type the following:
diskpart
Diskpart will open, in this terminal type:
# This will show all the drives on the computer
list disk
# Select the disk with the same storage capacity as the usb
# X - where x is the disk number of the usb
select disk X
clean
Then open "diskmgmt.msc" and format the unused volume using the wizard.
After this the usb should "cleaned"