A new type of void-like structure has been identified in thin 3C-SiC heteroepitaxial layers grown on silicon substrates. Similar surface structures can be found in micrographs published in the literature but have not been addressed so far. We propose a mechanism which explains the formation of these “type II voids” as result of hot-hydrogen etching. Type II voids seem to act as nucleation sites for the well-known faceted voids formed beneath the 3C-SiC layer during seeding (type I voids). Suppression of type II voids by appropriate high temperature cleaning steps therefore reduces the overall density of detrimental type I voids.