Physically-based photoresist models, such as those in PROLITH, have been very successful in describing photolithography from a continuum standpoint. These models allow engineers to accurately predict the final resist CD on the wafer and to analyze process robustness, such as calculation of focus-exposure process windows. However, as feature sizes continue to shrink, we are beginning to see yield-limiting phenomena that are due to the molecular nature of photoresist materials. One example of this is line-edge roughness (LER). LER is believed to be due to fluctuations during the exposure process (shot noise) and post-exposure bake (thermal diffusion and reaction). We present a model that explicitly takes into account the molecular nature of the photoresist during the exposure and post-exposure bake processes. We do this by writing a master equation that describes the probability that acid molecules are generated during exposure, and then describes the evolution of the acid, quencher, and blocking-group probability distributions during the bake process. We show how all the parameters in this model can be simply derived from the parameters in a calibrated PROLITH continuum model. Finally, we demonstrate prediction of LER from an accurately tuned PROLITH continuum model and compare the LER predictions with experimental results.