Hypersonic boundary layer flow during Stardust entry is simulated over Thermal Protection System (TPS) microstructure using the Direct Simulation Monte Carlo (DSMC) method. During the ablation process, the thermal stresses and traction forces acting on the TPS microstructure, combined with its oxidation, could affect its structural integrity. Hence, the local surface properties, namely, heat flux and traction force acting on the microstructure are estimated, studied and compared to estimates from Computation Fluid Dynamics (CFD). Preliminary simulations have been performed on different microstructures varying in porosity, orientation and diameter of fibers to study its effect on the surface properties. The capability of DSMC to compute relevant surface properties required for thermo-structural material response studies of TPS structures is demonstrated.