How do I encrypt an external drive with FileVault 2 in OSX Yosemite
I understand that you're running into issues, so this is going to be more for others looking for info on this topic. Encrypting non-boot volumes should be a relatively easy process in OS X 10.8.x and later.
To encrypt a non-boot volume:
Right-click on the volume you want to encrypt
Select the Encrypt… command
- When prompted, enter a password and (optionally) a password hint.
The drive will momentarily disappear from the desktop (to initialize the encryption) then re-appear.
I wanted to mention that this process will not work on your Flash drive as it comes formatted as a FAT Partition. You will need to reformat the drive to Mac OS Extended (Journaled) then when you enable the Encryption it will be be converted to Mac OS Extended (Journaled, Encrypted)
You will be able to reformat your flash drive using Disk Utility found in your /Applications/Utilities folder.