A method for removing material from a substrate includes providing the substrate with first and second opposing major surfaces. A masking layer is disposed along one of the first major surface and the second major surface, and is provided with a plurality of openings. The substrate is placed within an etching apparatus and material is removed from the substrate through openings using the etching apparatus. The thickness of the substrate is measured within the etching apparatus using a thickness transducer. The measured thickness is compared to a predetermined thickness and the material removal step is terminated responsive to the measured thickness corresponding to the predetermined thickness. In one embodiment, the method is used to more accurately form recessed regions in semiconductor die, which can be used in, for example, stacked device configurations.