A method and system are disclosed for finding virtual tooth features on virtual three-dimensional models of the teeth of patients. The tooth features comprise marginal ridges, cusp tips, contact points, central groove and buccal groove. Tooth axes system plays a key role in identifying the tooth features. An iterative method is disclosed for improving the accuracy of the tooth axes system. A virtual three-dimension model preferably obtained by scanning the dentition of a patient forms the basis for determining the tooth features. Tooth features are derived for all categories of teeth including molars, premolars, canines and front teeth. Tooth features are very helpful and used in planning orthodontic treatment. The tooth features are determined automatically using the computerized techniques; and can be manually adjusted when necessary.