1. A method for creating a physical three dimensional (3D) model, comprising: (a) using a computer system: providing a three dimensional (3D) virtual model of a patient's dentition including virtual model components corresponding to at least a part of each upper and lower jaw thereof and comprising virtual dental surfaces including at least a region of the teeth that includes a tooth stump on which a crown or a bridge is to be fitted; providing 3D data representative of at least the spatial relationship between said jaws in occlusion; incorporating in said 3D virtual model, one or more digitally created structural reference components comprising a first structure of the upper jaw that couples together with a second structure of the lower jaw so as to define an alignment arrangement for said 3D virtual model based on said 3D data, thereby defining an updated 3D virtual model, said one or more structural reference components configured to provide virtual occlusion alignment between said model components according to the spatial relationship; and (b) following step (a), preparing a physical three dimensional (3D) model including physical model components that respectively represent said virtual model components, based on said updated 3D virtual model obtained in step (a), wherein said physical model components are produced incorporating one or more physical structural reference components respectively corresponding to said one or more digitally created structural reference components to enable selectively providing physical occlusion alignment between said physical model components corresponding to said virtual occlusion alignment.