The effect of protruding microstructures/granules from non-porous carbon ablators in a high-speed flowfield is studied to characterize the concentration of oxidation products in the boundary layer and to understand the effect of microstructure on macroscopic surface reaction rates. Numerical simulations are performed using Direct Simulation Monte Carlo (DSMC), a stochastic particle-based technique able to accurately model the flow at small length scales including gas-surface interactions occurring at the micro-scale. Two different studies are performed; convection-diffusion within a boundary layer and also an isolated diffusion study. For both cases, gas-phase reactions are neglected, however, probabilities of surface reaction are applied to each particle-surface collision, and are referred to as microscopic probabilities. Both studies reveal that for high microscopic probabilities, the concentration of oxidation products in the boundary layer is not sensitive to changes in microstructure or reaction probabilities, and thus, the surface reactions are limited only by the diffusion of reactants towards the surface from the boundary layer. For low microscopic probabilities, the surface reactions clearly become reaction limited where changes in the microstructure surface area and reaction probabilities significantly affect the concentration of oxidation products in the boundary layer. It is further observed that an increase in total surface area due to the microstructure does not correspond to an equivalent increase in the net rate of surface reactions, due to the interplay between diffusion and surface reaction within the microstructure.