A laser surgery system having a computer control system coupled to a laser subsystem and a patient seat. The control system is coupled to the laser through a laser alignment system. The control system can be coupled to the patient seat through a patient alignment system. The control system sends a nominal position signal to move the patient seat, laser subsystem, or both so that the patient's first eye is moved into substantial alignment with the laser beam axis. The control system can send a second nominal signal to move the patient's second eye into substantial alignment with the laser beam axis. The control system can optionally comprise both an operator display and an assistant display. The assistant display provides real-time information to an assistant positioned at an assistant station adjacent the patient seat. The control system can be programmed to display edit fields with different colors to provide an obvious indication of the refractive information of the eye. The control system can comprise an operator input for providing a pre-determined secondary ablative treatment. If it is determined that the first ablative treatment did not completely remove the epithelial layer from a target region, the operator actuates the operator input to deliver the secondary ablative treatment.