In recent years, the technology of traditional integrated circuit fabrication is facing a huge challenge. As the top-down lithography gradually approaches to its size limit, the development of atomic-scale precise fabrication for functional devices has already become a major scientific issue at present and might become a breakthrough in the development of information technology in the future. With the reference of the bottom-up self-assembly, which is the basic principle of constructing various advanced structures in living systems, the integrated assembly of atoms can be gradually constructed through a series of operations such as capturing, positioning, and moving atoms. The advent of framework nucleic acids (FNAs) happens to provide a new platform for manipulating single atom or integrating multiple atoms. As is well known, the nucleic acids are not only the carriers of genetic information, but also biological building blocks for constructing novel microscopic and macroscopic materials. The FNAs represent a new type of framework with special properties and features, constructed by nucleic acids’ bottom-up self-assembly. With the improvement of chemical synthesis and modification method of nucleic acids, various molecules and materials, such as fluorophores, nanoparticles, proteins, and lipids, can be spatially organized on FNAs with atomic precision, and these functionalized FNAs have been widely explored in the fields of biosensing, biocomputing, nano-imaging, information storage, nanodevices, etc. Based on the features of precise addressability, superior programmability and tailorable functionality, FNAs can be used for implementing the artificial self-assembly of objects with atomic precision to realize the precise arrangement in spatial and functional integration of basic assembly units, and even prompt the development of device fabrication from atomic scale to macroscopic scale. This review focuses on the intersection of FNAs and atomic fabrication, giving a systematically description of the feasibility and advantages of precisely atomic fabrication with FNAs from three aspects. First, the DNA/RNA nanoarchitectures from static state to dynamic state and general strategies for programmable functionalization of FNAs are briefly introduced. Then the applications of FNAs in device fabrication are highlighted, including single molecule reactors, single molecule sensors, nanodevices for cargo loading and transporting, nanophotonics, nanoelectronics and information processing devices. Finally, an outlook of the future development of atomic fabrication with FNAs is given as well.