A method of forming thin film waveguide regions in lithium niobate uses an ion implant process to create an etch stop at a predetermined distance below the lithium niobate surface. Subsequent to the ion implantation, a heat treatment process is used to modify the etch rate of the implanted layer to be in the range of about 20 times slower than the bulk lithium niobate material. A conventional etch process (such as a wet chemical etch) can then be used to remove the virgin substrate material and will naturally stop when the implanted material is reached. By driving the ions only a shallow distance into the substrate, a backside etch can be used to remove most of the lithium niobate material and thus form an extremely thin film waveguide that is defined by the depth of the ion implant. Other structural features (e.g., ridge waveguides) may also be formed using this method.