One of the best and recommended methods is encrypting your files or encrypting the drive itself, so that nobody can access it without a proper password. There are several programs available for this, one such application is Rohos Mini Drive.
Rohos Mini Drive creates hidden and encrypted virtual partition on the USB flash drive. You can store any file here and can be work with these files without opening a special program.
Creating a hidden virtual drive is very easy with this program. Intuitive Setup Wizard automatically detects your USB flash drive and setup encrypted partition properties. You just need to provide a protection password. Encryption is automatic and on-the-fly. The help file along with the program teaches you more about it.
Rohos Mini Drive program does not create real partition on the USB flash drive. Thus when you insert your USB drive into USB port only one drive letter will appear in Windows. Second (secured) drive will appear only after you active it by entering a password.More details and download from the program page