You can encrypt individual folders by making an archive and encrypting that. The file system shouldn't matter for this.
In Nautilus, right click on a folder, and choose "Compress..." Then in the pop up modal dialog you can choose your compression method and whether or not to encrypt it. By default on Fedora, only ZIP encryption is offered.
Nautilus requires the Seahorse plugins to support TAR files. I'm trying that now.
This is all Gnome specific. I assume KDE has a way to do this, too.