A method for manufacturing multiple layers of waveguides is disclosed. Initially, a first cladding layer is deposited on a substrate, a first inner cladding layer is then deposited on the first cladding layer, and a first waveguide material is deposited on the first inner cladding layer. The first inner cladding layer and the first waveguide material are then selectively etched to form a first waveguide layer. Next, a second inner cladding layer followed by a second cladding layer are deposited on the first waveguide layer. The second inner cladding layer and the second cladding layer are removed by using a chemical-mechanical polishing process selective to the first waveguide material. A third inner cladding layer followed by a second waveguide material are deposited on the first waveguide material. The third inner cladding layer and the second waveguide material are then selectively etched to form a second waveguide layer. Finally, a fourth inner cladding layer followed by a third cladding layer are deposited on the second waveguide layer.