Linux Poison posted a guide about using eCryptfs (Cryptographic Filesystem) in Ubuntu Linux

eCryptfs is a kernel-native stacked cryptographic filesystem for Linux. Stacked filesystems layer on top of existing mounted filesystems that are referred to as lower filesystems. eCryptfs is a stacked filesystem that encrypts and decrypts the files as they are written to or read from the lower filesystem.

  How to use eCryptfs (Cryptographic Filesystem) in Ubuntu Linux