Provided is a method of patterning structures on a substrate using an integration scheme in a patterning system, the method comprising: disposing a substrate in a processing chamber, the substrate having a plurality of structures and a pattern, the substrate including an underlying layer and a target layer, at least one structure intersecting with another structure, each intersection having an intersection angle and a corner, the integration scheme requiring a vertical corner profile at each intersection; alternatingly and sequentially etching and cleaning the substrate to transfer the pattern onto the target layer and to achieve a target vertical corner profile at each intersection; controlling selected two or more operating variables of the integration scheme in the alternating and sequential etching and cleaning operations in order to achieve target integration objectives.