Numerical results are presented for the stability analysis of the wake induced by a cuboidal roughness element mounted on a flat plate inside a Mach 6 freestream. Linear BiGlobal stability calculations are carried out for a single frequency on a spanwise plane located behind the roughness, using base flows obtained from laminar Navier–Stokes simulations. The results show that the Mack mode is the most unstable perturbation growing in the boundary layer, followed by varicose and sinuous deformations of the low-velocity streak that characterizes the wake flow structure. The shock wave induced at the leading edge of the flat plate is found to have a significant stabilizing effect on the flow field. The use of a higher wall temperature stabilizes the Mack mode but increases the growth rate of the varicose perturbation.