Nano-materials and devices designed by programmed self-organization processes are presented in a realistic style. The concept of programmed self-organization is the accumulation of elemental self-assembling steps with the control of time, space, and geometry by sequential procedures, fusion of top-down and bottom up processes, and multi-dimensional crystal growth, respectively. Molecule-incorporated DNA was formed by specific molecular recognition through the use of triple hydrogen bonding. For the construction of network-based molecular-scale devices, we developed the DNA-templated arrangement of Au-nanoparticles and top-contact electrode using nano-transfer printing. We also found that self-organized positioning of functional lipid vesicles on nano-well electrodes is useful for electrochemical bio-sensing.