A method of forming a substrate with isolation areas suitable for integration of electronic and photonic devices is provided. A common reticle and photolithographic technique is used to fabricate a mask defining openings for etching first and second areas in a substrate, with the openings for the second trench isolation areas being wider than the openings for the first trench isolation areas. The first and second trench isolation areas are etched in the substrate through the mask and filled with an oxide material. The oxide material is removed from the bottom of the second trench isolation areas. The second trench isolation areas are further etched to the deeper than the first trench isolation areas, and are then filled with oxide material. Electrical devices can be formed on the substrate and electrically isolated by the first trench isolation areas and photonic devices can be formed over the second trench isolation areas and be optically isolated from the substrate.