A realistic aircraft wing is not expected to be an ideally smooth surface: the influence of junctions or wing panels must be taken into account in the laminar wing design. The presence of these spanwise invariant two-dimensional surface irregularities further amplifies the boundary-layer streamwise instabilities existing on a smooth surface, potentially causing an early transition to turbulence. In the present work, the effect of steps, gaps and humps on the development of Tollmien-Schlichting (TS) waves in an incompressible boundary layer is studied using direct numerical simulations (DNS). For a specific height we investigated several shapes of the geometric irregularity. Depending on their shape the surface imperfections give rise to a local separation bubble which interacts with the oncoming TS waves: for the frequency considered, all the surface irregularities have a destabilizing effect, with the rectangular hump case being the most dangerous one.