A method includes receiving, into a measurement tool, a substrate having a material feature, wherein the material feature is formed on the substrate according to a design feature. The method further includes applying a source signal on the material feature, collecting a response signal from the material feature by using the measurement tool, and with a computer connected to the measurement tool, calculating a simulated response signal from the design feature. The method further includes, with the computer, in response to determining that a difference between the collected response signal and the simulated response signal exceeds a predetermined value, causing the measurement tool to re-measure the material feature.