providing a substrate layer;

providing a mesa layer on top of the substrate layer;

etching a selected portion of the mesa layer to define a lower alignment mark having a lower trench region;

depositing a coating layer above the lower alignment mark, the coating layer being substantially conformal, wherein an upper trench region is formed in an upper portion of the coating layer above the lower trench region;

depositing an amorphous carbon layer on the coating layer; and

exposing portions of the amorphous carbon layer to a dose of radiation so as to elevate a top surface region of the amorphous carbon layer located above the lower trench region in the lower alignment mark, such that said top surface region is higher than adjacent portions of the top surface of the amorphous carbon layer, wherein said top surface region comprises an upper alignment mark located at a same horizontal position as the lower alignment mark.