1. A system for generating a digital model of teeth, comprising: a processor operably coupled to a computer readable storage medium comprising instructions which, when executed, cause the processor to: (a) receive 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 preparation region of the teeth; receive 3D data representative of at least the spatial relationship between the upper and lower jaws in occlusion; incorporate in the 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 the 3D virtual model based on the 3D data, thereby defining an updated 3D virtual model, the one or more structural reference components configured to provide virtual occlusion alignment between the virtual model components according to the spatial relationship; and (b) following step (a), output data for preparing a physical three dimensional (3D) model, the data including virtual model components that respectively represent physical model components based on the updated 3D virtual model obtained in step (a), wherein the physical model components include one or more physical structural reference components respectively corresponding to the one or more digitally created structural reference components to enable selectively providing physical occlusion alignment between the physical model components corresponding to the virtual occlusion alignment.