A system for assisting users in orthodontic diagnosis and treatment comprising: a computing device; and modeling software executing on the computing device, wherein the modeling software comprises: a rendering engine; a user interface that visually displays a 3D digital representation of a patient's teeth as well as a 3D digital representation of an orthodontic appliance, wherein the orthodontic appliance is a bracket, and provides an interface for receiving input from a user for manipulating a tooth or bracket, wherein the user interface receives user input indicating a desired movement for the tooth, wherein the movement refers to the overall movement of the tooth from a first position to a second position; an orthodontic appliance control module to translate and apply the inputted movement to calculate a new position of the bracket associated with the tooth, characterized in that the orthodontic appliance control module translates the desired tooth movement to movement of the bracket by reversing the direction of desired movement inputted by the user; and a tooth control module calculates a new tooth position based on the adjusted position of the bracket and moves the tooth accordingly, wherein the user perceives that he or she is directly moving the tooth within the 3D environment. a computing device; and modeling software executing on the computing device, wherein the modeling software comprises: a rendering engine; a user interface that visually displays a 3D digital representation of a patient's teeth as well as a 3D digital representation of an orthodontic appliance, wherein the orthodontic appliance is a bracket, and provides an interface for receiving input from a user for manipulating a tooth or bracket, wherein the user interface receives user input indicating a desired movement for the tooth, wherein the movement refers to the overall movement of the tooth from a first position to a second position; an orthodontic appliance control module to translate and apply the inputted movement to calculate a new position of the bracket associated with the tooth, characterized in that the orthodontic appliance control module translates the desired tooth movement to movement of the bracket by reversing the direction of desired movement inputted by the user; and a tooth control module calculates a new tooth position based on the adjusted position of the bracket and moves the tooth accordingly, wherein the user perceives that he or she is directly moving the tooth within the 3D environment. a rendering engine; a user interface that visually displays a 3D digital representation of a patient's teeth as well as a 3D digital representation of an orthodontic appliance, wherein the orthodontic appliance is a bracket, and provides an interface for receiving input from a user for manipulating a tooth or bracket, wherein the user interface receives user input indicating a desired movement for the tooth, wherein the movement refers to the overall movement of the tooth from a first position to a second position; an orthodontic appliance control module to translate and apply the inputted movement to calculate a new position of the bracket associated with the tooth, characterized in that the orthodontic appliance control module translates the desired tooth movement to movement of the bracket by reversing the direction of desired movement inputted by the user; and a tooth control module calculates a new tooth position based on the adjusted position of the bracket and moves the tooth accordingly, wherein the user perceives that he or she is directly moving the tooth within the 3D environment.