A closed-loop control system for altering the optical characteristics of a patient's cornea includes an algorithm for predicting the shape of the cornea after one or more gas bubbles resulting from intrastromal photoablation have collapsed. Patient data can be used as an input for the algorithm, which is then run to prepare an initial treatment plan for a corneal alteration. The initial plan typically includes a plurality of intrastromal photoablation locations and corresponding ablation energies. After photoablation of plan location(s) and before the resulting bubbles collapse, a real-time wavefront shape for light passing through the cornea is measured. The wavefront is then used in the algorithm to predict a post bubble collapse cornea shape and to generate an updated treatment plan. The procedure then continues by ablating location(s) identified in the updated treatment plan. Wavefront measurement and plan updating can be repeated as many times as desired.