1. An apparatus for generating image maps from 3D image data obtained from imaging an eye, said eye having at least one boundary surface associated therewith, said apparatus comprising: an optical coherence tomography (OCT) system, said system including a light source, a beam splitter for dividing the light along a sample arm and a reference arm, said sample arm further including optical elements to scan the beam over the eye, said OCT device including a detector for receiving light returned from both the sample and the reference arms and generating signals corresponding to 3D image data based on an axial reflection distribution arising from reflecting features in the eye; and a processor for identifying the boundary surface within the 3D image data, selecting at least one region of the boundary surface, and generating a substantially smooth reference surface using the at least one selected region of the boundary surface, said processor for identifying a second surface within the 3D image data and calculating the distance between points on the smooth reference surface and corresponding points on the second surface and generating an image map of the calculated distances.