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Nanomechatronics is a new emerging field at the intersection of nanotechnology and mechatronics. In this paper, control methods for nanomechatronic systems with respect to signaling, structure, and functions are reviewed, where control techniques that have been applied to nanobiosystems are presented. As an important example of nanomechatronic systems, molecular motors are discussed in terms of informatics and biophysics, respectively. A computational biological study on signaling pathways for the control of molecular motors in neurons is given to demonstrate a controller structure for nanomechatronics. As an extreme control method for living cells, a genome-level synthetic biotechnology is summarized. On the perspective of nanomechatronics, key factors of moleware robotics are examined toward the innovation of new nanorobots, which is one of the most promising applications of nanomechatronics in the new millennium.