The smart-cut™ process is based on inducing and processing structural defects below the free surface of semiconductor wafers. The necessary defects are currently induced by implantation of light elements such as hydrogen or helium. An alternative softer way to induce shallow subsurface defects is by RF-plasma hydrogenation. To facilitate the smart-cut process, the wafers containing the induced defects need to be subjected to an appropriate thermal treatment. In our experiments, (0 0 1) Si wafers are submitted to 200 and 50 W hydrogen RF-plasma and are subsequently annealed. The samples are studied by transmission electron microscopy (TEM), before and after annealing. The plasma-introduced defects are {1 1 1} and {1 0 0} planar-like defects and nanocavities, all of them involving hydrogen. Many nanocavities are aligned into strings almost parallel to the wafer surface. The annealing is performed either by furnace thermal treatment at 550 °C, or by in situ heating in the electron microscope at 450, 650 and 800 °C during the TEM observations. The TEM microstructural studies indicate a partial healing of the planar defects and a size increase of the nanometric cavities by a coalescence process of the small neighbouring nanocavities. By annealing, the lined up nanometric voids forming chains in the as-hydrogenated sample coalesced into well-defined cracks, mostly parallel to the wafer surface.