A pen drive can be made bootable using different methods and tools but the most used ones are WintoFlash and Unebootin. One is for making USB drives bootable for Windows environment and the second for Linux. Basing on your needs, you can use Wintoflash for everything related to Windows XP, Vista, 7, 8 versions or Unebootin for almost all major Linux distributions. In both cases, upon starting of the software a wizard will guide you along the way for a successful operation.