The present work describes the efforts to model a complex microstructure of an Avcoat-like material using direct simulation Monte Carlo (DSMC) method with correct boundary conditions, where a cross flow of boundary layer and pyrolysis species through the material can be simulated. To aid in choosing the gas pressures at the boundary, the development and verification of a continuum scale, finite volume solver is presented that models the gas phase in conjunction with the solid phase. To understand the thermal response of the microstructure, a hybrid random walk model is described, which has a capability to include convection, conduction, and radiation. With the help of these tools, the relative importance of heat transfer mechanisms is analyzed on a micron scale morphology. Using DSMC, the continuum permeability of 15.7×10−12 m2 is obtained for our microstructure model with 0.71 porosity. Furthermore, the flow through the microstructure during the process of pyrolysis is analyzed and the detailed collision statistics are reported as a function of depth. An estimate of collision statistics along an assumed trajectory is given to show the relative importance of gas-gas and gas-surface collisions. In addition, a way to scale the DSMC results on a small scale sample to larger depths is described. Finally, molecular dynamics (MD) simulations based on reactive-force-field (ReaxFF) potential are performed to elucidate the pyrolysis kinetics of a highly crosslinked phenolic formaldehyde resin.