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Your computer system views a USB drive or other removable device as another hard drive partition. Just like any other drive mounted on your system, you can encrypt it as a whole or in part and often with the same software used to protect the other more permanent or fixed hard drives on your system. The same goes for whatever operating system you run –Windows, UNIX, Linux or even on a Mac.
Additionally, the entire device can be password-protected without encrypting individual connections, and it's also possible to encrypt drives that already contain files.
There's a wide range of free and commercially available products that will suit your needs. All you have to do is encrypt the virtual partition on your file system that represents the USB or removable device. There are many drive encryption products on the market and you should base your choice on the size and needs of your organization. Also, make sure the product uses the most current and strongest encryption algorithms, preferably with 128-bit encryption or better, like AES.
Tools with this level of encryption include Private Disk and Secrets Keeper from Dekart, CruzerLock from SanDisk, DataTraveler Elite Privacy Edition from Kingston and SafeGuard PrivateDisk from Utimaco Software. Another recently released product from Hexprobe is their Storage Encryption Tool that password protects any removable drive or device with 128-bit AES.
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