A method, structure, system of aligning a substrate to a photomask. The method includes: directing incident light through a pattern of clear regions transparent to the incident light in an opaque-to-the-incident-light region of a photomask, through a lens and onto a photodiode formed in a substrate, the photodiodes electrically connected to a light emitting diode formed in the substrate, the light emitting diode emitting light of different wavelength than a wavelength of the incident lights; measuring an intensity of emitted light from light emitting diode; and adjusting alignment of the photomask to the substrate based on the measured intensity of emitted light.