A simulator for e-beam exposure and development (SELID) is combined with molecular modeling in order to investigate the various side effects of the gelation process in the case of chemically amplified resists (CARs). The procedure is demonstrated in the case of the negative tone epoxy resist but the method is equally applicable for other resist systems (positive and negative tone) and development mechanisms. A conventional resist simulator is not sufficient for the description of characteristics related to the detailed gel structure of the resist film and it needs to be combined with a molecular model. Molecular modeling is a suitable method for the simulation of the microscopic changes occurring during the post-exposure bake and development processes in the case of CARs. Macroscopic feature changes such as free volume size, cluster formation, and surface roughness can be effectively described using percolation theory. In order to construct a molecular model of a complex resist system a 3D square lattice is considered. The lattice size is equal to the mean radius of the spherical volume occupied by a monomer, in our case about 1 nm. The lattice is filled with the polymer chains by a random walk process and the photoacid generator is randomly distributed in the lattice according to its percent content in the actual material. In the case of an actual resist pattern exposure, SELID provides the energy deposition profile after e-beam exposure. The deposited energy stored into each cell of the lattice induces acid generation and subsequent reactions. Reaction progress is simulated using the molecular model. Using the above process it has been possible to reproduce the actual experimental contrast curves and to simulate line edge roughness.