A molecular scale simulation of the pattern formation process for chemically amplified resist in electron beam lithography based on the stochastic approach is proposed. The initial resist structures are formed by the sequential bonding of the randomly selected monomers. The effects of electron exposure are introduced by the activation of the acid generator which randomly determined according to the absorbed energy distribution in the resist. The absorbed energy distribution is calculated using the Monte Carlo simulation of electron scattering. The effects of the post exposure bake are introduced by the acid diffusion and the polymer deprotection reactions. The fundamental properties, such as quencher concentration dependence, molecular weight dependence, and exposure condition effects on pattern profiles, are well reproduced by the simulation.