A method of blink detection in a laser eye surgical system includes providing a topography measurement structure having a geometric marker. The method includes bringing the topography measurement structure into a position proximal to an eye such that light traveling from the geometric marker is capable of reflecting off a refractive structure of the eye of the patient, and also detecting the light reflected from the structure of the eye for a predetermined time period while the topography measurement structure is at the proximal position. The method further includes converting the light reflected from the surface of the eye into image data and analyzing the image data to determine whether light reflected from the geometric marker is present is in the reflected light, wherein if the geometric marker is determined not to be present, the patient is identified as having blinked during the predetermined time.