A method for reconstructing an ear canal from optical coherence tomography (OCT) scan data of an ear comprises extracting frame numbers and line numbers of interference intensities corresponding to one or more markers on an OCT scan guide, receiving reference frame numbers and lines numbers for one or more markers, determining a starting position and direction for the OCT ear scan from the ear scan marker frame and line numbers and the reference marker frame and line numbers, for each scan line, finding a pixel number of a maximum interference intensity value, and determining an offset distance of said pixel from said scan guide, and reconstructing a surface of the ear canal from the distance offset data.