Techniques, apparatus and systems are described for wafer-scale processing of aligned nanotube devices and integrated circuits. In one aspect, a method can include growing aligned nanotubes on at least one of a wafer-scale quartz substrate or a wafer-scale sapphire substrate. The method can include transferring the grown aligned nanotubes onto a target substrate. Also, the method can include fabricating at least one device based on the transferred nanotubes.