To encrypt folders on Linux Ubuntu there is a simple program called Cryptkeeper which, while active, lets you mount and dismount password protected folders.
While unmounted, the encrypted folders are invisible to the user. While mounted, you need to enter the password to access its contents. To create a new encrypted folder just click on the key icon on the system panel and select New encrypted folder.
Make sure to unmount the encrypted folders before you quit Cryptkeeper since the files become accessible if they are mounted and Cryptkeeper is inactive. The files remain invisible if they are unmounted and Cryptkeeper is quit.