Do you specifically mean an X.509 certificate? If so, I think some custom coding work may be in order on your part. There's nothing particularly challenging about that, but I don't fully see the point.
Flash drives (or any encrypted disk image) are encrypted using symmetric encryption. Certificates are based around public key encryption. I would suggest using some sort of certificate-based (or PGP) file encryption to encrypt a keyfile for the drive image if you're trying to securely share a disk image across an insecure channel.
It is possible to design a system (PGP Whole Disk Encryption comes to mind) where the symmetric key for the drive is natively guarded by public keys. I'm not aware of any other products that do this, but you might be able to find some via Google.