A method of correcting optical coherence tomography (OCT) image data obtained from a layered media sample includes identifying at least one interface from the obtained OCT data and correcting the OCT data for distortion at the at least one interface. The OCT image data can be corrected for extrinsic distortions, such as those caused by scan geometry, as well as, intrinsic distortions, such as those caused by refraction at each interface.