A method of designing hearing aid molds is disclosed whereby skeletons, or simplified models, of two ear impressions are used to register the graphical representations of the molds to facilitate the joint design of hearing aid shells. The center points of at least a portion of contour lines on the surface of each ear impression are identified. Then, for each ear impression, by connecting these center points to each adjacent center point, a skeleton that represents a simplified model of an ear impression is generated. Vectors describing the distance and direction from the points of each skeleton to an anatomical feature of each ear impression are identified to obtain a correspondence between the points of each skeleton. Three-dimensional translations and rotations of a feature vector of at least one of the skeletons are determined to achieve alignment of the skeleton of one ear impression with the skeleton of another impression.