Like traditional keying, the 3D Keyer in the Modular Keyer and Batch is used to select a range of colours to key out, such as the blue or green background in a clip. In the 3D Keyer, however, this range of colours is represented visually in an RGB viewer. You can use the RGB viewer to analyse the colour areas in a clip, and then refine the key with increased accuracy.
The 3D Keyer can be used for many purposes other than pulling a key from the key-in clip. For example, in the Modular Keyer, you could use the Keyer-3D node in the Matte pipe of the CBlend node to isolate a region of the front clip to which you want to apply a particular colour correction.