Is there a way to add a password to an existing external folder?

I use an external drive to make a mirrored backup of all my work files. But some of my projects are confidential so I keep those files encrypted and in a separate hard-drive.

Is there a way to encrypt or use a very, very secure password-thingie so I can keep all my files in the same place? I'd also need something that could work with my syncing application, because I sync my files several times a week. I know that some of those apps won't work if the folders are password-protected.