1. A computer-implemented method for the detection of deviations from an orthodontic treatment plan, comprising: receiving a tracking model comprising a non-segmented digital representation of an actual arrangement of a patient's teeth after an orthodontic treatment plan has begun for the patient for comparison to a previously segmented plan model comprising a segmented digital representation of a pre-determined planned arrangement of the patient's teeth; performing a first alignment of the non-segmented digital representation of the actual arrangement and the segmented digital representation of the pre-determined planned arrangement such that teeth in the segmented digital representation of the pre-determined planned arrangement are positioned to substantially match corresponding tooth positions in the non-segmented digital representation of the actual arrangement, the first alignment comprising: a rough matching comprising automatically detecting a structural feature from the non-segmented digital representation of the actual arrangement previously unidentified in the tracking model and a structural feature from the segmented digital representation of the pre-determined planned arrangement, and rough aligning the non-segmented digital representation of the the actual arrangement and the segmented digital representation of the pre-determined planned arrangement based on the detected structural features; and a fine aligning of the non-segmented digital representation of the actual arrangement and the segmented digital representation of the pre-determined planned arrangement, the fine aligning comprising matching a surface of the non-segmented digital representation of the actual arrangement and a surface of the segmented digital representation of the pre-determined planned arrangement; performing a second alignment of the non-segmented digital representation of the actual arrangement and the segmented digital representation of the pre-determined planned arrangement, comprising: comparing the non-segmented digital representation of the actual arrangement with the segmented digital representation of the pre-determined planned arrangement so as to detect stationary elements of the patient's dentition such that positions of one or more non-stationary teeth are measurable relative to the detected stationary elements, and re-aligning the non-segmented digital representation of the actual arrangement and the segmented digital representation of the pre-determined planned arrangement based on the detected stationary elements; and detecting, based on the non-segmented digital representation of the actual arrangement and the segmented digital representation of the pre-determined planned arrangement as aligned per the second alignment, one or more positional differences between the actual arrangement of the patient's teeth and the pre-determined planned arrangement of the patient's teeth.