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Erosion of carbon surfaces due to oxidation does not occur uniformly but through the formation of localized etch pits because of active surface sites. These active sites are formed due to the presence of atomic defects on the carbon surface and have much higher reactivity compared to average non-defective sites. Thus, these active sites are the first to react during ablation, resulting in their removal. This causes all the neighboring atoms to be defective, and increasing their reactivity, thus leading to localized carbon removal around these “active” sites. In this manner, these highly reactive defects serve as nucleation sites for the formation and growth of etch pits, with detrimental effects on the structural integrity. In order to understand the influence of these etch pits on the material properties of carbon fiber microstructures, we have developed a new capability within direct simulation Monte Carlo (DSMC) to capture the etch pit formation process. This capability is developed within the DSMC code SPARTA (Stochastic PArallel Rarefied-gas Time-accurate Analyzer) and can model the material removal in the presence of active sites leading to the formation of etch pits. The focus of the current work will be to study the effect of etch pits on the material properties of FiberForm, the precursor substrate of the PICA Thermal Protection System (TPS) material. The microstructure of virgin FiberForm obtained directly from X-ray microtomography scans is used within SPARTA to obtain the ablated geometries with etch pits. These pitted microstructures are then imported into the Porous Microstructure Analysis (PuMA) software and various material properties such as thermal conductivity, elasticity, and permeability are computed. The variation of these properties because of the complex evolution of the surface topology due to the formation of etch pits is studied and analyzed. Furthermore, the effect of pitting is compared to the case of uniform radial shrinking of fibers, which has been the standard for modelling ablation of carbon structures, and significant differences are observed. Thus, a physically realistic model of material removal through the formation of etch pits will be helpful in predicting the degradation of carbon-based TPS more accurately during oxidation; as well as other mechanisms such as spallation, which involves the removal of chunks of material into the flow due to the growth of etch pits. This will ultimately improve our understanding of the failure modes in these materials due to ablation.