A ophthalmic laser-assisted corneal lenticule extraction procedure that uses wavefront measurements to guide the formation of the corneal lenticule. The wavefront map measured from a free eye using a wavefront aberrometer is registered to the cornea of a docked eye based on comparisons of iris images and corneal markings. The docked-eye cornea-registered wavefront map is then corrected to be consistent with the Munnerlyn formula for the spherical power, and adjusted for any physician adjustments and/or myopia error due to a flat add in the lenticule, using Zernike polynomials. The corrected and adjusted wavefront map is then used to calculate the profiles of the bottom and top lenticule incisions in the applanated cornea, where higher-order components in the wavefront map are distributed to the bottom lenticule incision alone and lower-order components in the wavefront map are distributed to both the bottom and the top lenticule incision.