Previous experimental and numerical studies showed that two-dimensional roughness elements can stabilize disturbances inside a hypersonic boundary layer and eventually delay the transition onset. The objective of this paper is to evaluate the response of disturbances propagating inside a high-speed boundary layer to various two-dimensional surface deformations of different shapes. We perform an assessment of the impact of various two-dimensional surface nonuniformities, such as backward or forward steps, combinations of backward and forward steps, wavy surfaces, surface dips, and surface humps. Disturbances inside a Mach 5.92 flat-plate boundary layer are excited using periodic wall blowing and suction at an upstream location. The numerical tools consist of a high-accuracy numerical algorithm solving for the unsteady, compressible form of the Navier–Stokes equations in curvilinear coordinates. Results show that all types of surface nonuniformities are able to reduce the amplitude of boundary-layer disturbances to a certain degree. The amount of disturbance energy reduction is related to the type of pressure gradients that are posed by the deformation (adverse or favorable). A possible cause (among others) of the disturbance energy reduction inside the boundary layer is presumed to be the result of a partial deviation of the kinetic energy to the external flow, along the discontinuity that is generated by the wall deformation.