A system for use in diagnosis and planning treatment of a human patient, comprising: a general purpose computer system having a processor and a user interface; a memory accessible to said general purpose computer system storing a) a first set of digital data representing patient craniofacial image information obtained from a first imaging device, and b) a second set of digital data representing patient craniofacial image information obtained from a second image device (30, 36) different from said first image device, said first and second sets of data (24, 26) representing at least in part common craniofacial anatomical structures of said patient, at least one of said first and second sets of digital data (24, 26) including data representing the external visual appearance or surface configuration of the face of the patient; and a set of computer instructions stored on a machine readable storage medium (22, 32) accessible to said general purpose computer system, wherein said set of instructions comprises instructions for causing said general computer system to: 1) automatically, and/or with the aid of operator interaction, superimpose said first set of digital data and said second set of digital data so as to create a composite, combined digital representation of said craniofacial anatomical structures in a common coordinate system; and 2) display said composite, combined digital representation of said craniofacial anatomical structures to a user of said system; characterized in that said set of instructions further comprises instructions for movement of said craniofacial structures and display of said movement in a dynamic format on said user interface, wherein the obtained virtual patient model is displayed and current smile of the patient is viewed, and changes to the smile are simulated by the simulation of tooth movement and its effect on soft tissue and its effect on the smile, the simulation is performed as a dynamic simulation, in which the series of changes into position, and their effect on soft tissue during the smile, is demonstrated in a manner showing the motion of the teeth and tissues. a general purpose computer system having a processor and a user interface; a memory accessible to said general purpose computer system storing a) a first set of digital data representing patient craniofacial image information obtained from a first imaging device, and b) a second set of digital data representing patient craniofacial image information obtained from a second image device (30, 36) different from said first image device, said first and second sets of data (24, 26) representing at least in part common craniofacial anatomical structures of said patient, at least one of said first and second sets of digital data (24, 26) including data representing the external visual appearance or surface configuration of the face of the patient; and a set of computer instructions stored on a machine readable storage medium (22, 32) accessible to said general purpose computer system, wherein said set of instructions comprises instructions for causing said general computer system to: 1) automatically, and/or with the aid of operator interaction, superimpose said first set of digital data and said second set of digital data so as to create a composite, combined digital representation of said craniofacial anatomical structures in a common coordinate system; and 2) display said composite, combined digital representation of said craniofacial anatomical structures to a user of said system; 1) automatically, and/or with the aid of operator interaction, superimpose said first set of digital data and said second set of digital data so as to create a composite, combined digital representation of said craniofacial anatomical structures in a common coordinate system; and 2) display said composite, combined digital representation of said craniofacial anatomical structures to a user of said system; characterized in that said set of instructions further comprises instructions for movement of said craniofacial structures and display of said movement in a dynamic format on said user interface, wherein the obtained virtual patient model is displayed and current smile of the patient is viewed, and changes to the smile are simulated by the simulation of tooth movement and its effect on soft tissue and its effect on the smile, the simulation is performed as a dynamic simulation, in which the series of changes into position, and their effect on soft tissue during the smile, is demonstrated in a manner showing the motion of the teeth and tissues.