A system and method for processing stroke-based handwriting data for the purposes of automatically scoring and clustering the handwritten data to form letter prototypes. The present invention includes a method for processing digitized stroke-based handwriting data of known character strings, where each of the character strings is represented by a plurality of mathematical feature vectors. In this method, each one of the plurality of feature vectors is labelled as corresponding to a particular character in the character strings. A trajectory is then formed for each one of the plurality of feature vectors labelled as corresponding to a particular character. After the trajectories are formed, a distance value is calculated for each pair of trajectories corresponding to the particular character using dynamic time warping method. The trajectories which are within a sufficiently small distance of each other are grouped to form a plurality of clusters. The clusters are used to define handwriting prototypes which identify subcategories of the character.