A key factor in the vertical integration of optical waveguide devices is the uniformity of the surface across which the coupling takes place. This thesis focuses on the fabrication of annealed proton-exchanged (APE) waveguides vertically integrated with chalcogenide waveguides. While titanium diffused waveguides form a surface bump that is approximately twice the size of the originally deposited film, an annealed proton-exchange process produces waveguides with surfaces having 90% less deformation. The theory behind wave guiding devices is explored in this work along with the modeling and simulation of APE waveguides. The results obtained from the simulations are used to aid in the fabrication of these devices. A detailed review of the fabrication process of APE waveguides and chalcogenide waveguides is provided with results obtained from measurements. The first known coupling results for vertically integrated chalcogenide waveguides on top of annealed proton-exchanged waveguides are recorded. This work is concluded with future directions for this research including lowering losses by obtaining better simulation parameters and vertically integrating ring resonators along with ways in which to do this.