An apparatus for determining a depth measurement and incising a cornea, the cornea having a photodisruption threshold, the apparatus comprising: a laser subsystem configured to scan a laser spot between the anterior surface of the cornea and the posterior surface of the cornea, the laser spot having an energy below the photodisruption threshold of the cornea; a first input operable to receive a first input signal indicating a focal depth of a laser beam within the cornea, the laser beam having an energy below the photodisruption threshold; a second input operable to receive a second input signal representing a harmonic of the laser beam generated as the laser beam propagates in the cornea; an output; and a processor coupled to the first input, the second input, and the output, the processor configured to: detect a pre-determined change in the second input signal, the pre-determined change indicating a tissue layer interface within the cornea; correlate the focal depth of the laser beam with the tissue layer transition to provide a reference depth of the laser beam; and transmit an output signal via the output, the output signal indicating the reference depth of the laser beam, characterized in that the laser subsystem is arranged to: output a pulsed incision beam having a pulse energy of greater than or equal to the photodisruption threshold, and incise the cornea with the pulsed incision beam based on the tissue layer transition. a laser subsystem configured to scan a laser spot between the anterior surface of the cornea and the posterior surface of the cornea, the laser spot having an energy below the photodisruption threshold of the cornea; a first input operable to receive a first input signal indicating a focal depth of a laser beam within the cornea, the laser beam having an energy below the photodisruption threshold; a second input operable to receive a second input signal representing a harmonic of the laser beam generated as the laser beam propagates in the cornea; an output; and a processor coupled to the first input, the second input, and the output, the processor configured to: detect a pre-determined change in the second input signal, the pre-determined change indicating a tissue layer interface within the cornea; correlate the focal depth of the laser beam with the tissue layer transition to provide a reference depth of the laser beam; and transmit an output signal via the output, the output signal indicating the reference depth of the laser beam, detect a pre-determined change in the second input signal, the pre-determined change indicating a tissue layer interface within the cornea; correlate the focal depth of the laser beam with the tissue layer transition to provide a reference depth of the laser beam; and transmit an output signal via the output, the output signal indicating the reference depth of the laser beam, characterized in that the laser subsystem is arranged to: output a pulsed incision beam having a pulse energy of greater than or equal to the photodisruption threshold, and incise the cornea with the pulsed incision beam based on the tissue layer transition. output a pulsed incision beam having a pulse energy of greater than or equal to the photodisruption threshold, and incise the cornea with the pulsed incision beam based on the tissue layer transition.