When making nano-sized materials, the conventional top-down approach of using tools to fabricate structures is fraught with problems. Because the tools need to be one or two orders smaller than the materials they are sculpting, sub-nano-sized tools are needed to make nano-sized structures by the top-down approach, and this is impossible. Top-down methods, such as microetching and other techniques using chemical reactions, are used in processes of hundreds of nanometers in scale, but the limit of usefulness of top-down methods is about 50 nm.

To carry out nanomanufacturing below such a limit, all sorts of bottom-up methods for building structures from smaller components are under consideration. One of those is the use of SPMs to actually manipulate and assemble atoms. However, there are high expectations for various other methods, including self-assembly-based thin-film growth technologies, such as molecular beam epitaxy and chemical vapor deposition (CVD), as well as nanomachining and other technologies for nano-sized processing.