The effects of rarefaction on hypersonic boundary layer flow over various discrete surface roughness configurations are examined parametrically for M∞ = 3.0 flow over a flat plate. The roughness heights are chosen such that the local Knudsen number (Kn = λ/k) in the region of the roughness are O(10-2), where k is the height of the protuberance and λ is the molecular mean free path. In this regime, the continuum approximations of zero velocity and no thermal slip at the wall begin to break down, and thermal non-equilibrium effects may become more prominent due to a relative increase in time required for thermal equilibration. The aim of this work is to address the significance of rarefaction effects in modeling the disturbance field generated by hypersonic boundary layer flow over surface roughness using a hybrid of the DAC and DPLR numerical simulation codes. Parametric studies have been conducted to examine flow over a flat plate with a smooth, oblique fence-like roughness for a M ∞= 3.0 five-species air flow over a flat plate. The radius of curvature at the top of the roughness is varied to examine the influence of this parameter on the flowfield and distributed surface quantities. Hybrid DAC solutions are generated and compared to the DPLR solutions generated with slip and no-slip wall conditions. The vibrational non-equilibrium observed in the shock, expansion and shear layer regions surrounding the roughness is found to impact the pressure at the surface, and the DPLR slip model predicts higher velocity slip near the expansion region at the surface of the roughness. The total heat flux on the surface of the protuberance is also examined. It is found that the hybrid DAC solution predicts a heating augmentation to the roughness that is 20 - 30% below the DPLR slip wall solution, and 30 - 50% below the DPLR no-slip wall solution for the roughness configurations examined.