In order to be useful as microelectromechanical devices, carbon nanotubes with well-controlled properties and orientations should be made at high density and be placed at predefined locations. We address this challenge by hierarchically assembling carbon nanotubes into closely packed and highly aligned three-dimensional wafer films from which a wide range of complex and three-dimensional nanotube structures were lithographically fabricated. These include carbon nanotube islands on substrates, suspended sheets and beams, and three-dimensional cantilevers, all of which exist as single cohesive units with useful mechanical and electrical properties. Every fabrication step is both parallel and scalable, which makes it easy to further integrate these structures into functional three-dimensional nanodevice systems. Our approach opens up new ways to make economical and scalable devices with unprecedented structural complexity and functionality.