Maybe I got myself misunderstood by using terms inappropriately; by "filesystem" I meant \root files. I'll use plain terms:
I want to save a directory (say "/home/DIR"), and all it's subdirectories, to a external HD. I want these files to be encrypted on this HD so I, only, can read them with the appropriate "key". Then, additionally, once I mount the HD, I'd like to rsync "/home/DIR" to the HD so it doesn't take hours each time to save the directory.
I'll have a look at ccrypt ASAP; then back to you. Cheers,