1. A computing device implemented method of using an individualized orthodontic treatment index, comprising: receiving an initial virtual dental model from a first scan of a patient's dentition; modifying the initial virtual dental model to create a target virtual dental model according to a treatment goal; assigning a number of dental references to the target virtual dental model; receiving a treatment outcome virtual dental model from a second scan of the patient's dentition; mapping the number of dental references from the target virtual dental model to the treatment outcome virtual dental model; and calculating an individualized treatment index score for the treatment outcome virtual dental model according to one or more differences between the target virtual dental model and the treatment outcome virtual dental model based on the number of dental references; wherein the method is performed by the computing device.