The first step of the smart‐cut™ process consists in inducing structural defects below the free surface of a silicon wafer, usually by implantation of light elements, such as hydrogen or helium. An alternative way to induce subsurface defects is by plasma treatment. In this work, we present a morphological and structural study on silicon wafers submitted to hydrogen plasma treatment, using two plasma‐processing geometries. The parameters of the plasma treatment have been varied in order to limit the surface roughness and to confine the induced defects in a narrow region (50 nm) below the wafer surface. The morphological and structural investigations have been performed by AFM and TEM.