A system and method are provided in which an iris or eye image is taken during a refractive diagnostic analysis. The image is employed for aligning data from the analysis with data from other refractive analysis instruments, as well as aligning a refractive surgical tool, such as a laser, with the eye for treatment. Further, the stored iris image is compared with the patient's iris before treatment, verifying that the correct eye is to be treated with a developed treatment pattern. A variety of refractive instruments can be used, such as corneal topography systems and wavefront aberration systems.