A method for processing a wafer, comprising: forming a mask on a microstructure, the mask including a first pattern that is positioned over a first region of the microstructure and a second pattern that is positioned over a second region of the microstructure; performing a first etching process, the first etching process etching the microstructure according to the first and second patterns (126, 124) formed in the mask to transfer the first and second patterns (126, 124) of the mask into the first and second regions (100b, 100a) of the microstructure, respectively; forming a protective layer over the first pattern of the mask that is positioned over the first region of the microstructure subsequently to the first etching process; performing a second etching process, the second etching process etching the microstructure and transferring the second pattern of the mask further into the second region of the microstructure; and removing the mask and the protective layer from the microstructure, wherein the first region of the microstructure is protected by the protective layer during the second etching process, wherein the first region of the microstructure comprises at least a channel region and comprises a plurality of top channel contacts within a dielectric layer, wherein performing the first etching process further comprises: transferring the first pattern of the mask into the first region to expose the plurality of top channel contacts and form a plurality of channel contact openings within the dielectric layer; and transferring the second pattern of the mask into the second region to form a plurality of trenches in the dielectric layer, the trenches having side portions and bottom portions; and wherein forming the protective layer over the first pattern of the mask comprises: forming the protective layer to fill the plurality of channel contact openings, wherein the protective layer further is accumulated on a top surface of the first pattern of the mask, and is uniformly formed along side portions and bottom portions of the trenches in the second region of the microstructure. forming a mask on a microstructure, the mask including a first pattern that is positioned over a first region of the microstructure and a second pattern that is positioned over a second region of the microstructure; performing a first etching process, the first etching process etching the microstructure according to the first and second patterns (126, 124) formed in the mask to transfer the first and second patterns (126, 124) of the mask into the first and second regions (100b, 100a) of the microstructure, respectively; forming a protective layer over the first pattern of the mask that is positioned over the first region of the microstructure subsequently to the first etching process; performing a second etching process, the second etching process etching the microstructure and transferring the second pattern of the mask further into the second region of the microstructure; and removing the mask and the protective layer from the microstructure, wherein the first region of the microstructure is protected by the protective layer during the second etching process, wherein the first region of the microstructure comprises at least a channel region and comprises a plurality of top channel contacts within a dielectric layer, wherein performing the first etching process further comprises: transferring the first pattern of the mask into the first region to expose the plurality of top channel contacts and form a plurality of channel contact openings within the dielectric layer; and transferring the second pattern of the mask into the second region to form a plurality of trenches in the dielectric layer, the trenches having side portions and bottom portions; and wherein forming the protective layer over the first pattern of the mask comprises: forming the protective layer to fill the plurality of channel contact openings, wherein the protective layer further is accumulated on a top surface of the first pattern of the mask, and is uniformly formed along side portions and bottom portions of the trenches in the second region of the microstructure. transferring the first pattern of the mask into the first region to expose the plurality of top channel contacts and form a plurality of channel contact openings within the dielectric layer; and transferring the second pattern of the mask into the second region to form a plurality of trenches in the dielectric layer, the trenches having side portions and bottom portions; and wherein forming the protective layer over the first pattern of the mask comprises: forming the protective layer to fill the plurality of channel contact openings, wherein the protective layer further is accumulated on a top surface of the first pattern of the mask, and is uniformly formed along side portions and bottom portions of the trenches in the second region of the microstructure.