Disclosed is an improved double patterning method for forming openings (e.g., vias or trenches) or mesas on a substrate. This method avoids the wafer topography effects seen in prior art double patterning techniques by ensuring that the substrate itself is only subjected to a single etch process. Specifically, in the method, a first mask layer is formed on the substrate and processed such that it has a doped region and multiple undoped regions within the doped region. Then, either the undoped regions or the doped region can be selectively removed in order to form a mask pattern above the substrate. Once the mask pattern is formed, an etch process can be performed to transfer the mask pattern into the substrate. Depending upon whether the undoped regions are removed or the doped region is removed, the mask pattern will form openings (e.g., vias or trenches) or mesas, respectively, on the substrate.