A system for treating an eye having a cornea, pupil and iris, the system comprising: an ophthalmic diagnostic device having a first image capture device for obtaining a first image of the eye during a diagnostic procedure; a femtosecond laser system having a second image capture device for obtaining a second image of the eye during formation of a laser corneal incision for forming a corneal flap, the corneal incision referenced to the first image; a processor system coupling the diagnostic device to the laser system, the processor system configured to direct laser energy from the laser system toward the eye during use by comparing the first image with the second image so as to register the corneal incision with the eye, characterized in that the processor system is further configured to generate a refractive laser treatment in response to the diagnostic procedure, to determine a desired corneal incision comprising determining a desired corneal flap referenced to the first image, wherein the desired corneal flap has a desired flap center and a desired rotationally asymmetric feature referenced to the first image, wherein the laser corneal incision defines a corneal flap having a flap center and a rotationally asymmetric feature; and the system further comprises a refractive reshaping laser system configured to capture a third image, to register the refractive laser treatment with the third image by determining an X-Y offset between the desired flap center referenced to the first image and the flap center in the third image, and to determine an angular offset between a desired flap angle referenced to the first image and the rotationally asymmetric feature in the third image. an ophthalmic diagnostic device having a first image capture device for obtaining a first image of the eye during a diagnostic procedure; a femtosecond laser system having a second image capture device for obtaining a second image of the eye during formation of a laser corneal incision for forming a corneal flap, the corneal incision referenced to the first image; a processor system coupling the diagnostic device to the laser system, the processor system configured to direct laser energy from the laser system toward the eye during use by comparing the first image with the second image so as to register the corneal incision with the eye, characterized in that the processor system is further configured to generate a refractive laser treatment in response to the diagnostic procedure, to determine a desired corneal incision comprising determining a desired corneal flap referenced to the first image, wherein the desired corneal flap has a desired flap center and a desired rotationally asymmetric feature referenced to the first image, wherein the laser corneal incision defines a corneal flap having a flap center and a rotationally asymmetric feature; a refractive reshaping laser system configured to capture a third image, to register the refractive laser treatment with the third image by determining an X-Y offset between the desired flap center referenced to the first image and the flap center in the third image, and to determine an angular offset between a desired flap angle referenced to the first image and the rotationally asymmetric feature in the third image.