A method for fabricating selectively coupled optical waveguides on a substrate is disclosed. Initially, a first layer of waveguide material is deposited on a substrate. The first layer of waveguide material is then etched to form multiple level one waveguides and fill shapes. A dielectric layer is deposited on top of the level one waveguides and fill shapes. The surface profile of the dielectric layer deposition tracks the pattern density of the fill shapes. After the surface of the dielectric layer has been polished, a second layer of waveguide material is deposited on the substrate. At least one optically coupled waveguide structure, which is formed by a first level one waveguide and a first level two waveguide, is located adjacent to at least one non-optically coupled waveguide structure, which is formed by a second level one waveguide and a second level two waveguide.