Not by building finer and finer tools. Self-assembly.
- Reverse-engineering. Organic chemistry.
- Engineering. Devise a small set of operations that build a systematic set of molecules, use this to build up desired molecules.
- Science. Brute force exploration of possibility space, find simple reactions that produce molecules with desired qualities. Wolfram's experiments show this is a possibility.
Probably a combination of all three. Exploration would first proceed using computer simulation. Software is freely available for such simulation, a wrapper would need to be written to enumerate possibilities and evaluate the outcome. Likely candidates would then be physically synthesized.
Tile-set based designs are an alternative to organic chemistry. A (quasi-)crystal that either is itself a computation or that is some kind of circuit that can perform computation, such as an FPGA. In order to assert a regular underlying structure, Tiff suggests basing the tile molecules around a metal atom. This is somewhat engineerable, in that there are known things that can be stuck to metal atoms, but would still require some brute-forcing.
Note that existing chip fabrication is already close to 2D nano-fabrication -- achieved essentially by the "finer and finer tools" route. The advantage of self-assembly would be the ability to build 3D structures.