A scatterometric sensor measures the intensity of light diffracted from a periodic structure. When applied in-situ to the post exposure bake (PEB) process for chemically amplified resists, a scatterometric sensor can monitor the formation of a latent image. Sturtevant, et al and Miller, et al have shown that this application of scatterometry is viable for chemically amplified resist linewidth, or critical dimension (CD) control. A CD control system requires the prediction of the final developed CD using data collected throughout part of the PEB process. Previous work has not addressed the issue of variations in underlying film thickness; these variations may not dramatically affect latent images when anti-reflection coatings are used, but they can greatly affect the signals from scatterometric sensors. This requires a sensor design coupled to a CD prediction algorithm that can accommodate underlying film thickness variations. We have designed, constructed and tested an experimental scatterometric sensor for the PEB process which collects sufficient data to provide a robust CD prediction. The instrument was installed on a PEB module at SEMATECH, and the signals from 0.35 micrometer linewidth gratings were measured on bare silicon (Si) wafers and wafers with varying poly-Si and oxide thicknesses. Using data from the first 45 seconds of a nominal 60 second PEB, final developed linewidth predictions were achieved with a standard error of prediction of 5.08 nm for bare Si wafers and 6.89 nm for poly-Si/oxide/Si wafers. In parallel with our sensor development effort, we have developed a physical model for diffraction from latent image gratings during the PEB process. The model links a lithography simulation tool to rigorous coupled wave diffraction theory. Diffraction from a latent image grating occurs via two mechanisms: variations of the index of refraction within the resist and a slight surface- relief grating which results from dose-dependent volume loss within the resist. Simulations indicate that the surface-relief grating dominates first-order diffraction signals.