Seems pretty straightforward. Pay some small software company to develop a custom encryption program for you. Then only systems you designate would have the program to encrypt/decrypt the files.
You wouldn't likely be able to encrypt the drive itself, since that would require some sort of encrypted filesystem. On Windows that leaves you with EFS, which is a bit dangerous if you're not careful, or having someone write a custom filesystem for you, which would probably be expensive and problematic at best.
I am looking for a soulution to have flash drives encrypted at work. I would also like the files on the flash drive to only be accessible while it is pluged into a computer at one of our five branch offices. Any suggestions? Thank you in advance. We are currently running XP on our machines and Server 03 however we are currently in the process of upgrading to Windows 7 and Server 08