Recent research has shown that 2-D roughness of finite height can damp the second mode instability under certain conditions. For instance, it has been shown that the relative location of 2-D roughness element and the synchronization point is important in determining the 2-D roughness effect on modal growth. It was found that if a roughness element is placed downstream of a disturbance's synchronization point, the disturbance is damped. In this paper, an extensive DNS parametric study on the effect of second mode instability from roughness height, width and spacing between roughness elements are conducted. The results reveal that a taller roughness within one boundary layer thickness height results a stronger damping effect on the second mode. On the other hand, the roughness width effect is relatively insignificant compared with the height effect. Lastly, the spacing between roughness elements has been studied. The results show the increasing in spacing of roughness elements has both advantages and disadvantages. For the second mode control using 2-D roughness elements, roughness elements spacing of 10 times the roughness width has been shown to have the best overall damping effect in a broad frequency bandwidth. Overall, our extensive study has shown that roughness height is an important factor for the amplification/damping effect. For a second mode control design using 2-D roughness, the roughness height of 50% boundary layer thickness, width of 2 boundary layer thicknesss and spacing of 10 have been chosen to optimize the damping mechanism. Ideally the laminar-turbulent transition process can be divided into four stages. The first involves small disturbance fields which are initialized via a process termed "receptivity" by the viscous flow. The initial disturbance fields can involve both freestream and vehicle self-induced fluctuations such as acoustics, dynamic vortices, entropy spottiness, etc. The next stage is the linear growth stage, where small disturbances are amplified until they reach certain amplitude where nonlinear effects become important. The amplification can be in the form of exponential growth of eigenmodes (Tollmien-Schlichting waves or Mack waves) and non-modal growth of optimal disturbances (Transient growth). Once a disturbance has reached a finite amplitude, it often saturates and transforms the flow into a new, possibly unsteady state, which is termed as the secondary instability stage. The last