Optical coherence tomography (OCT) is used to map the surface elevation and thickness of the cornea. The OCT maps are used to plan laser procedures for the treatment of an irregular, opacified or weakened cornea, and in the treatment of refractive errors. In the excimer laser phototherapeutic keratectomy (PTK) procedure, the OCT data is used to plan a map of ablation depth needed to restore a smooth optical surface. In the excimer laser photorefractive keratectomy procedure, OCT mapping of epithelial thickness is used to achieve clean laser epithelial removal. In femtosecond laser anterior keratoplasty procedure, OCT data is used to plan the depth of femtosecond laser dissection to remove an anterior layer of the cornea, leaving a smooth recipient bed of uniform thickness to receive a disk of donated corneal tissue. The linkage of an OCT system to a precise laser surgical system enables the performance of new procedures that are safer, less invasive and produce faster visual recovery than conventional surgical procedures.