The current invention is directed to a method of patterning a surface or layer in the fabrication of a micro-device. In accordance with a preferred embodiment of the invention, a first mask structure is formed by depositing a layer of a first material onto the surface or layer and embossing the layer with a micro-stamp structure. The layer is preferably embossed as a liquid, which is solidified or cured to form the first mask structure. The first mask structure can be used as an etch-stop mask which is removed in a subsequent processing step or, alternatively, the first mask structure can remain a functional layer of the micro-device. In further embodiments, unmasked regions of the surface or layer are chemically treated through the first mask structure and/or a second material is deposited onto the unmasked regions of the surface or layer through the first mask structure to form a second mask structure and/or a second functional layer of the micro-device.