One of the major challenges in commercializable micro-nano systems development is the high cost and turnaround that are incurred through multiple product-optimization iterations and expensive fabrication processes for specific systems. Development of complex and heterogeneous micro-nano systems, that are only possible through assembly and not by conventional surface machining approaches, are further impeded by lack of standard design rules and off-the-shelf robotic manipulation systems. Dedicated hardware and system specific component designs, although possible, are not commercially viable for addressing the wide range of opportunities that exists in the prevailing micro-nano domain. In this paper, we present an alternative and holistic top-down approach for micro-nano manufacturing using modular part designs and flexible assembly systems. We incorporate, seamlessly, multiple novel algorithms related to microrobotics and scaling of physics, obtained both analytically as well as experimentally; in order to predict, track and control the uncertainty propagation in a typical manufacturing process, in micro-nano scale, throughout production steps including design, machining, setup, assembly, testing etc. We demonstrate, through multiple examples, the implementation of the proposed framework in micro-nano scale manufacturing.