Você pode fazer isso usando discos de loopback criptografados por GPG . Esta página explica o conceito da seguinte forma:
My intention was to be able to secure some data by encrypting them with a GPG key, but not have to create a new partition on my disk. Also, I wanted to do easy backups by just backing up a single file. I also wanted to be sure that I would still be able to recover everything in case my disk encryption GPG key was lost. Since I am not aware of any systems that do this automatically, I just combined loopback devices, luks and GPG into a set of bash scripts.