The current understanding and research efforts on surface roughness effects in hypersonic boundary-layer flows focus, almost exclusively, on how roughness elements trip a hypersonic boundary layer to turbulence. However, there were a few reports in the literature suggesting that roughness elements in hypersonic boundary-layer flows could sometimes suppress the transition process and delay the formation of turbulent flow. These reports were not common and had not attracted much attention from the research community. Furthermore, the mechanisms of how the delay and stabilization happened were unknown. A recent study by Duan et al. showed that when 2-D roughness elements were placed downstream of the so-called synchronization point, the unstable second-mode wave in a hypersonic boundary layer was damped. Since the second-mode wave is typically the most dangerous and dominant unstable mode in a hypersonic boundary layer for sharp geometries at a zero angle of attack, this result has pointed to an explanation on how roughness elements delay transition in a hypersonic boundary layer. Such an understanding can potentially have significant practical applications for the development of passive flow control techniques to suppress hypersonic boundary-layer transition, for the purpose of aero-heating reduction. Nevertheless, the previous study was preliminary because only one particular flow condition with one fixed roughness parameter was considered. The study also lacked an examination on the mechanism of the damping effect of the second mode by roughness. Hence, the objective of the current research is to conduct an extensive investigation of the effects of 2-D roughness elements on the growth of instability waves in a hypersonic boundary layer. The goal is to provide a full physical picture of how and when 2-D roughness elements stabilize a hypersonic boundary layer. Rigorous parametric studies using numerical simulation, linear stability theory (LST), and parabolized stability equation (PSE) are performed to ensure the fidelity of the data and to study the relevant flow physics. All results unanimously confirm the conclusion that the relative location of the synchronization point with respect to the roughness element determines the roughness effect on the second mode. Namely, a roughness placed upstream of the synchronization point amplifies the unstable waves while placing a roughness downstream of the synchronization point damps the second-mode waves. The parametric study also shows that a tall roughness element within the local boundary-layer thickness results in a stronger damping effect, while the effect of the roughness width is relatively insignificant compared with the other roughness parameters. On the other hand, the fact that both LST and PSE successfully predict the damping effect only by analyzing the meanflow suggests the mechanism of the damping is by the meanflow alteration due to the existence of roughness elements, rather than new mode generation. In addition to studying the unstable waves, the drag force and heating with and without roughness have been investigated by comparing the numerical simulation data with experimental correlations. It is shown that the increase in drag force generated by the Mach wave around a roughness element in a hypersonic boundary layer is insignificant compared to the reduction of drag force by suppressing turbulent flow. The study also shows that, for a cold wall flow which is the case for practical flight applications, the Stanton number decreases as roughness elements smooth out the temperature gradient in the wall-normal direction. Based on the knowledge of roughness elements damping the second mode gained from the current study, a novel passive transition control method using judiciously placed roughness elements has been developed, and patented, during the course of this research. The main idea of the control method is that, with a given geometry and flow condition, it is possible to find the most unstable second-mode frequency that can lead to transition. And by doing a theoretical analysis such as LST, the synchronization location for the most unstable frequency can be found. Roughness elements are then strategically placed downstream of the synchronization point to damp out this dangerous second-mode wave, thus stabilizing the boundary layer and suppressing the transition process. This method is later experimentally validated in Purdue's Mach 6 quiet wind tunnel. Overall, this research has not only provided details of when and how 2-D roughness stabilizes a hypersonic boundary layer, it also has led to a successful application of numerical simulation data to the development of a new roughness-based transition delay method, which could potentially have significant contributions to the design of future generation hypersonic vehicles.