An in-depth surface chemistry model is proposed for high-temperature oxidation of carbon-based thermal protection system materials. This work builds upon a recently developed finite-rate oxidation model by incorporating additional subsurface processes at the microscale including subsurface oxygen transport and the oxidation reaction front as a function of material depth. The direct simulation Monte Carlo (DSMC) code, SPARTA, is used to simulate the interaction of high temperature atomic oxygen within layers of graphene. Reaction rates are determined from the ten-mechanism finite rate model of Gopalan et al., while subsurface transport of oxygen via advection is modeled using a novel multilayer oxidation model. This multilayer oxidation code captures the competition between oxygen transport and carbon removal at material wall temperatures in the extreme temperatures of atmospheric reentry conditions, allowing for quantification of both subsurface oxygen concentration profiles and the reaction front. We present in-depth oxygen concentration profiles, reaction front and recession rates for a 1D configuration, and we discuss the implications and importance of a 3D configuration.