Three-dimensional (3D) printing has been an active area of research and development due to its capability to produce 3D objects by design. 3D printers are commercially available with resolution as high as micrometers. Further miniaturization to reach nanometer scale would require development of materials, instruments, and methodology to attain required spatial precision. This dissertation reports our recent progress in facilitating the development of 3D micro- and nano-printing technologies using atomic force microscopy (AFM)-based methods. Followed by introduction and description of techniques utilized in this dissertation, Chapter 3 describes a new 3D nanoprinting method via direct delivery based on an integrated atomic force microscopy (AFM) and microfluidic platform. This platform combines the high spatial precision of AFM with the direct delivery capability of microfluidics. Designed structures were printed layer-by-layer with intra- and inter-layer alignment reaching nanometer precision. The resulting 3D structures demonstrate high degree control over spatial and material delivery. Chapter 4 describes a new algorithm developed to enable construction and display of layer-by-layer 3D structures from scanning probe microscopy (SPM) images. The algorithm enables alignment of SPM images acquired during layer-by-layer deposition and removal of redundant features to faithfully construct the deposited 3D structures. The display uses a "see-through" strategy to make the structure of each layer to be visible. The results demonstrate high spatial accuracy and algorithm versatility. To the best of our knowledge, this represents the first report to enable SPM technology for 3D imaging construction and display. The detailed algorithm is provided to facilitate usage of the same approach in any SPM software. These new capabilities support wide application of SPM that require 3D image reconstruction and display, such as 3D nanoprinting, and 3D additive and subtractive manufacturing and imaging. Chapter 5 presents a new chemistry, referred to as "controlled assembly" developed based on our 3D printing technology. In this work, delivery of sub-fL solution onto a designed surface was achieved using our AFM/microfluidic platform, the rapid evaporation of solvent leads to assemblies of solute molecules. Controlled molecular assembly has previously been demonstrated using macromolecules in 0 dimension (0D). In this work, we pushed the limit of this control into smaller molecules using a tetrazine derivative (MW of 8.1 kD, hydrodynamic radius around 1.5 nm), and using patterned surfaces to further control the solution distribution. Control over molecular assemblies in both 0D and 1D cases were demonstrated. The three technology developments, collectively, bring us much closer to realize 3D nanoprinting with advanced applications such as in nanophotonics, nanoelectronics, micro- and nano-fluidic devices, new nanocomposite materials, and tissue engineering. In Chapter 6, production of custom-designed micro-droplets networks is demonstrated by delivery of water molecule in oil. Cell-sized micro droplets by design is easily produced and directly delivered to the designed locations under our setup. Further changes of the droplet network can also be achieved if necessary by moving individual droplets using the same probe to designated locations. This new method paves the way to study and prepare networks of bio-compartment and artificial cells, and contributes to a fundamental study to facilitate 3D nanoprinting in liquid phase. Finally, summary and future perspectives are provided in Chapter 7.