A molecular-based representation of a negative tone chemically amplified resist was developed and studied using stochastic simulations. The gel formation mechanism resulting from the reaction–diffusion phenomena in the polymer matrix during the postexposure bake step, as well as the surface and line-edge roughness formation were investigated in two dimensions. Graph theorycomputational techniques were employed to determine the gel cluster size and its relation to the fraction of the total number of chemically and physically cross-linked chains. Results of the simulation include the maximum aciddiffusion range, the cross-link density, the surface and line edge roughness, versus exposure dose and photoacid generator concentration.