By moving a substrate relative to a shadow mask in a reactive ion etching system, we are able to precisely tailor the thickness of critical layers. To minimize disturbing the plasma, all the mechanical components are kept below the anode. The system is highly reproducible, and can be programmed to yield arbitrary vertical profiles along one horizontal axis. Using silicon-on-insulator substrates, the resonance wavelength was modified as a function of position with better than 1 nm control in the vertical dimension. This technique should prove useful for optical devices where the thickness of the layers controls the device characteristics.