In order for the USB to boot to something, you need an ISO file of a bootable image. You didn't mention which tools you're using so I can't really specify a process.
Sardu lets you create a bootable disk if various ISO's that you download from within the program.
pendrivelinux.com has a few utilities (including links to Sardu) that allow you to create a bootable USB disk which will run one or several ISO images.
If you want to run Windows-based utilities from a bootable USB, I would suggest visiting UBCD4Win.com and downloading the utility. I use it a lot. It's still XP-based but it will run the typical tools (MBAM, SAS, Spybot, etc).