To encrypt a directory on Linux you can use encfs. You'll need two directories: a mount point, and a raw storage directory.
mkdir ~/mount-point mkdir ~/.encfs-raw
Then we'll need to setup encfs for these directories. The default options should be plenty secure for whatever you'll need.
encfs ~/mount-point ~/.encfs-raw
To unmount this encrypted directory use fusermount
fusermount -u ~/mount-point
To change the password on your encfs directory use encfsctl
encfsctl passwd ~/mount-point
Update: You can use the --idle command to automatically unmount the directory after X minutes of inactivity