Systems and methods for efficiently obtaining optical coherence tomography (OCT) measurement data with reduced effects of motion are presented. One embodiment involves determining the amount of motion present during the collection of an OCT data set based on images of the eye collected at the same time as the OCT data, and recollecting select portions of the OCT data set when the amount of eye motion is determined to exceed a predetermined threshold. Another embodiment includes enabling or disabling a tracking feature based on the quality of the images available for tracking. Another embodiment includes reducing the effect of motion in the axial direction based on a comparison to a model of the eye constructed from OCT data. The method can also be used to reduce the presence of mirror image artifacts in an OCT image.