An alignment system for aligning a wafer when lithographically fabricating LEDs having an LED wavelength λLED is disclosed. The system includes the wafer. The wafer has a roughened alignment mark with a root-mean-square (RMS) surface roughness σS. The system has a lens configured to superimpose an image of the reticle alignment mark with an image of the roughened alignment mark. The roughened alignment marked image is formed with alignment light having a wavelength λA that is in the range from about 2σS to about 8σS. An image sensor detects the superimposed image. An image processing unit processes the detected superimposed image to measure an alignment offset between the wafer and the reticle.