We have yet to see a really reliable method of 3D printing with multiple colors with FDM technology. One patent filed recently though shows quite the promise. The patent which can be read about here: http://3dprint.com/4877/patent-color...inter-filament is pretty clever if you ask me.

What it does is send printer filament through a colorizing mechanism prior to it getting heated by the extruder nozzle. This colors it just prior to building with the filament.

Could this work? Do you think we will see something like this any time soon? Check out the diagram of this patent below: