Three-dimensional (3D) printing has been a very active area of research and development due to its capability to produce 3D objects by design. Miniaturization and improvement of spatial resolution are major challenges in current 3D printing technology development. This work reports advances in miniaturizing 3D printing to the nanometer scale using scanning probe microscopy in conjunction with local material delivery. Using polyelectrolyte polymers and complexes, we have demonstrated the concept of layer-by-layer nanoprinting by design. Nanometer precision is achieved in all three dimensions, as well as in interlayer registry. The approach enables production of designed functional 3D materials with nanometer resolution and, as such, creates a platform for conducting scientific research in designed 3D nanoenvironments as well. In doing so, it enables production of nanomaterials and scaffolds for photonics devices, biomedicine, and tissue engineering.