Local disturbances caused by a spanwise surface corrugation affect the position of the boundary-layer transition, and so the drag, of an object. This premature transition from laminar to turbulent flow is often associated with a separation of the laminar boundary-layer from its surface. Also the roughness-induced separation bubble provides an important link between the pressure and velocity fluctuations in the environment and the development of the disturbance in the laminar boundary-layer, i.e., the receptivity problem. To investigate the influence of a laminar separation bubble on boundary-layer instability, a separated flow generated by a velocity gradient over a flat plate was analyzed by direct numerical simulation using finite-difference solutions of the Navier-Stokes equations. The bubble acts as a strong amplifier of the instability waves and a highly nonlinear flow field is shown to develop downstream of the bubble. Consequently, the results of the direct numerical simulation differ noticeably from those of the classical linear stability theory proving the fact that the nonparallel effects together with the nonlinear interactions are crucial to this flow development. In the present paper, the effect of physical perturbations such as humps and hollows on boundary-layer instability is analyzed. This problem has been considered theoretically by several researchers (e.g., Nayfeh et al., 1987 and 1990; Cebeci et al., 1988). They used linear stability theory in their approach which does not include the nonparallel nor the nonlinear effects. Therefore, to account for these important effects in studying flow over humps and hollows the direct simulation technique is being implemented in generalized coordinates.