1. A method for measuring the cornea of the eye with an optical coherence tomography system (OCT), said method comprising: collecting a first set of OCT data over a series of transverse locations on the cornea of the eye within a time short enough to avoid any significant motion of the cornea; processing the data collected in the first data set to generate a model of the cornea; collecting a second set of OCT data over a series of transverse locations on the cornea of the eye; determining one or both of the axial and transverse motion in the second data set by fitting the data in the second set to the model of the cornea created from the first set; creating a motion-corrected data set from the second data set using one or both of the determinations of axial and transverse motion; and storing or displaying of the motion-corrected data set or information derived from the motion-corrected data set.