A method of aligning a wafer when lithographically fabricating a light-emitting diode (LED). The method includes forming on the wafer at least one roughened alignment mark having a root-mean-square (RMS) surface roughness σS. The roughened alignment mark is formed as a consequence of forming a plasma etch to roughen a LED surface on which the wafer alignment mark resides. The method also includes imaging the at least one roughened wafer alignment mark with alignment light having a wavelength λA that is in the range from about 2σS to about 8σS. The method also includes comparing the detected image to an alignment reference to establish wafer alignment. Once wafer alignment is established, p-contacts and n-contacts can be formed on the LED upper surface in their proper locations.