Creating prototypes using machines are fun, but they needed a 3D model to be created and use as a reference. Models are not created equally, the can come from imagination, a design intent or derived from reverse engineering process.
In basic term, 3D model can be created from solid or surface model. although they are several formats that can be used during a model creation. for example, in a rapid prototyping process, the scanned file is basically a bunch of point clouds that is converted into meshes. if you reverse an organic model, maybe like a car bumper, ideally, it would be rebuild into a NURBS surface.
Below are several of 3D application that can be used for that purposes.