The minimization of nanoscale roughness in patterned images has become a priority for the process of photolithography in the production of microprocessors. In order to probe the molecular basis for surface roughness, the development of photoresist has been simulated through application of the critical-ionization model to a three-dimensional molecular lattice representation of the polymer matrix. The model was adapted to describe chemically amplified photoresists of the sort now commonly used in microlithography. Simulations of the dependence of the dissolution rate and surface roughness on the degree of polymerization, polydispersity, and fractional deprotection agree with experimental results. Changes in surface roughness are shown to correlate with the length of the experimentally observed induction period. Model predictions for the effect of void fraction and developer concentration on roughness are also presented. Observations of differences in the effect of developer concentration on top-surface and sidewall roughness are explained by a critical development time predicted by the simulation.