Large-area membranes consisting of arrays of gold metal nanotubes were used as shadow masks to generate vertical nanopatterned 6H-SiC(0001) substrates. The gold membranes are formed by a replication technique based on electrochemical deposition of anodic aluminium oxide membranes or silicon substrates containing lithographically generated etch pits. Using the gold metal membranes as masks in reactive ion etching, spatially well-resolved protrusions in the SiC substrate were etched, arranged in periodic and non-periodic two-dimensional arrays. Final vertical morphological reorganizations were obtained in a hot-wall reactor under hydrogen flow. The obtained large-area networks of nano-objects have many potential applications in magnetism, electronics and biology.