Pattern formation of pyrolyzed carbon (PyC) and tetrahedral amorphous carbon (ta-C) thin films were investigated at micro- and nanoscale. Micro- and nanopillars were fabricated from both materials, and their biocompatibility was studied with cell viability tests. Carbon materials are known to be very challenging to pattern. Here we demonstrate two approaches to create biocompatible carbon features. The microtopographies were 2 μm or 20 μm pillars (1:1 aspect ratio) with three different pillar layouts (square-grid, hexa-grid, or random-grid orientation). The nanoscale topography consisted of random nanopillars fabricated by maskless anisotropic etching. The PyC structures were fabricated with photolithography and embossing techniques in SU-8 photopolymer which was pyrolyzed in an inert atmosphere. The ta-C is a thin film coating, and the structures for it were fabricated on silicon substrates. Despite different fabrication methods, both materials were formed into comparable micro- and nanostructures. Mouse neural stem cells were cultured on the samples (without any coatings) and their viability was evaluated with colorimetric viability assay. All samples expressed good biocompatibility, but the topography has only a minor effect on viability. Two μm pillars in ta-C shows increased cell count and aggregation compared to planar ta-C reference sample. The presented materials and fabrication techniques are well suited for applications that require carbon chemistry and benefit from large surface area and topography, such as electrophysiological and -chemical sensors for in vivo and in vitro measurements.