1. A method comprising: 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; applying a source signal on the material feature by using a source in the measurement tool having a tool setting parameter; collecting a response signal from the material feature by using a detector in the measurement tool to obtain measurement data; with a computer connected to the measurement tool, calculating a simulated response signal from the design feature using the tool setting parameter; and 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.