The method performs a first photolithography and etch to form shallow trench isolation features and alignment mark features into the top SOI layer. The shallow trenches are then filled with a dielectric material to form the isolation. A second lithography and etch step is then applied to etch the window locations for back-side contacts, and to transfer the alignment marks down into the SOI lower substrate. After this first lithography and etch step, the alignment marks in the top silicon may be used for alignment of the second lithography mask and etch. This is made possible by leaving the polish stop layer on the wafer, which serves to increase the optically effective thickness of the alignment mark pattern. The polish stop layer is removed after the second etch process. The teachings can be applied to any Semiconductor-On-Insulator-type wafer/technology where the top semiconductor layer is not thicker than the optimum alignment mark depth.