A method for forming deep corneal lamellar incision parallel to the posterior corneal surface when the eye is docked to the patient interface. A lower-energy detecting beam generated by the same pulsed laser that generates the higher-energy treatment laser beam is utilized to measure the posterior corneal surface profile. The detecting beam is scanned in the eye according to a first 3-dimensional scan pattern, while intensity of the back-reflected light is measured by a light intensity detector. The first scan pattern may be a spiral pattern in the X-Y plane coupled with a Z direction oscillation function. Peaks of the light intensity signal are detected, and corresponding spatial positions of the focus point are obtained; a known offset distance is added to the depth value to obtain the posterior corneal surface profile. Based thereon, the treatment laser beam is scanned in the eye to form the deep corneal lamellar incision.