MicroSolved, Inc. – Security consultants (MicroSolved, Inc.) point out three ways to secure a USB drive.
geek.menu is a fork of the portableApps.com menu system. According to this blog post "Installed and configured right, it makes an encrypted file system to protect your data if you lose the drive. It also allows you to easily configure some pretty powerful options around the apps you install. Check it out if you are a big thumb drive user.
This article from Help Net Security is a great overview of risks from thumb drives. It should be a basic requirement for any user in the organization that gets provisioned one.
Last, for those of you want to make the most of security through obscurity to protect your precious USB thumb drive from discovery, check this article out about hiding your drive in the wall.
If you are both a thumb drive (USB drive) and a Windows user, you should probably read about the Conflicker malware. It is currently spreading wildly and can transit itself on USB drives. (Oooops, that was 4….)"