In Rapid prototyping you always work with a reference point. The reference point always works in a very direct manner. Methodologies involving rapid prototyping always require multiple operations. Main characteristics of such operations are energy exchange as well as complex chemistry.
For instance, you may take into account the number of the variables that are involved in exposure of photopolymer using laser in Stereo-lithography. You can easily determine the center point where the laser should strike. It may not be so easy with a cutting tool. That is the essence of rapid prototypes.
Energy that emits from the laser will create geometrically as well as chemically complex reaction within the body of the fluid. The reason is that laser contains non-uniform energy profile. The fluid on the other hand has optical properties that affects the reaction. Photopolymer also changes its phases turning into solid state. However in the process it might shrink quite a bit that might also cause internal stress in part. Thus the polymer cures would be affected by the previous layer and possibly also by exposure to the remaining liquid parts of the photopolymer.
These fluctuations prompt some of the experts to consider rapid prototyping as less accurate in comparison to CNC. However the truth is just the reverse. It has been proved time and again that despite multiple operations, rapid prototyping is not only accurate but much faster than the CNC. You can not expect to have custom-designed parts with CNC quickly in any case.