Micro- and nano-structuring have been highlighted over several decades in both science and engineering fields. In addition to continuous efforts in fabrication techniques, investigations in scalable nanomanufacturing have been pursued to achieve reduced feature size, fewer constraints in terms of materials and dimensional complexity, as well as improved process throughput. In this study, based on recent micro-/nanoscale fabrication processes, characteristics and key requirements for computer-aided design and manufacturing (CAD/CAM) systems for scalable nanomanufacturing were investigated. Requirements include a process knowledge database, standardized processing, active communication, adaptive interpolation, a consistent coordinate system, and management of peripheral devices. For scalable nanomanufacturing, it is important to consider the flexibility and expandability of each process, because hybrid and bridging processes represent effective ways to expand process capabilities. As an example, we describe a novel CAD/CAM system for hybrid three-dimensional (3D) printing at the nanoscale. This novel hybrid process was developed by bridging aerodynamically focused nanoparticle printing, focused ion beam milling, micromachining, and spin-coating processes. The system developed can print a full 3D structure using various inorganic materials, with a minimum process scale of 50 nm. The most obvious difference versus CAD/CAM at ‘conventional’ scales is that our system was developed based on a network to promote communication between users and process operators. With the network-based system, it is also possible to narrow the gap among different processes/resources. We anticipate that this approach can contribute to the development of CAD/CAM for scalable nanomanufacturing and a wide range of hybrid processes.