A method for laser eye surgery that accommodates patient movement includes: generating a first and a second electromagnetic radiation beam, the second beam configured to modify eye tissue; propagating the first beam to a scanner along a an optical path length that changes in response to eye movement; focusing the first beam to a first focal point within the eye; scanning the first focal point at different locations within the eye; propagating a portion of the first beam reflected from the first focal point location back along the variable optical path to a sensor; generating an intensity signal indicative of the intensity of the portion of the reflected first beam; propagating the second beam to the scanner along the variable optical path; focusing the second beam to a second focal point and scanning the second focal point to create an incision in the cornea of the eye.