You take a point and figure out if it needs to be colored differently based on certain criteria. Like if it was in shadow, or if it's being hit by a bright light, or you just want a sepia tone across everything. You can even shift everything. Take the screen and distort it according to some kind of function. Like make it all wavy.
3d games are no more or less conceptually different than 2d games in a lot of regards. There are more things to track and be aware of, but you're effectively doing a lot of the same things.
If you've ever messed around with making 2d games, you can even begin simple experimentation by just making another layer of depth. Like LittleBigPlanet, it's ostensibly a 2D game presented with 3D graphics. But it allows you to shift between 3 layers to give you some depth.