Methods for patterning of multi-depth layers for the fabrication of optical devices are provided. In one embodiment, a method is provided that includes disposing a resist layer over a device layer disposed over a top surface of a substrate, the device layer having a first portion and a second portion, patterning the resist layer to form a first resist layer pattern having a plurality of first openings and a second resist layer pattern having a plurality of second openings, and etching exposed portions of the device layer defined by the plurality of first openings and the plurality of second openings, wherein the plurality of first openings are configured to form at least a portion of a plurality of first structures within the optical device, and the plurality of second openings are configured to form at least a portion of a plurality of second structures within the optical device.