A method and apparatus for generating a three dimensional representation of an ear canal are disclosed whereby an ear canal of a patient is imaged using optical coherence tomography (OCT). In a first embodiment, cross-section images of an ear canal are taken by, for example, rotating an OCT imaging sensor about a predetermined axis at each of a plurality of positions. In accordance with another embodiment, a contour line is then identified in each of the cross section images and a flow algorithm is used to identify the boundary of the ear canal cross section. Once the boundaries of each cross section have been identified, all of the cross section images are combined to generate a three dimensional image of the ear canal.