A method for registering two three-dimensional shapes is disclosed whereby the two shapes are represented as zero level set of signed distance functions and the energy between these two functions is minimized. In a first embodiment, two undetailed ear impression models are rigidly registered with each other. In another embodiment, a detailed ear impression is initially aligned with an undetailed ear impression model and, then, the detailed ear impression model is rigidly registered with the undetailed ear impression model as a function of the signed distance functions. In accordance with another embodiment, an undetailed ear impression model is non-rigidly registered with a template ear impression model as a function of the signed distance functions.