Surface roughness is known to have a substantial impact on the aerothermodynamic loading of hypersonic vehicles, particularly via its influence on the laminar-turbulent transition process within the boundary layer. Numerical simulations are performed to investigate the effects of a distributed region of densely packed, smooth-shaped roughness elements on the laminar boundary layer over a 7-degree half-angle, circular cone for flow conditions corresponding to a selected trajectory point from the ascent phase of the HIFiRE-1 flight experiment. For peak-to-valley roughness heights of 50 percent or less in comparison with the thickness of the unperturbed boundary layer, the computations converge to a stationary flow, suggesting that the flow is globally stable.Analysis of convective instabilities in the wake of the roughness patch indicates two dominant families of unstable disturbances, namely, a high frequency mode that corresponds to Mack mode waves modified by the wake and a lower frequency mode that corresponds to shear layer instabilities associated with the streaks in the roughness wake. Even though the peak growth rate of the later mode is more than 35 percent greater than the peak growth rates of the Mack modes, the latter modes achieve higher amplification ratios, and hence, are likely to dominate the onset of transition, which is estimated to occur slightly later than that in the unperturbed, i.e., smooth surface boundary layer. Additional computations are performed to investigate the effects of various roughness patch configurations on a Mach 3.5 flat plate boundary layer, to help guide an upcoming experiment in the Mach 3.5 Supersonic Low Disturbance Tunnel at NASA Langley Research Center. In this case, the cumulative reinforcement of basic state distortion over the length of the roughness patch is predicted to yield a significantly earlier transition than that over a smooth plate or a plate with a shorter length roughness patch.