Micro-electromechanical systems (MEMS) as an enabling technology is seen to play a more and more important role for the main stream of industry of the future by broadening its applications to information, communications and bio technologies. Development of MEMS devices, however, still relies on knowledge and experience of MEMS experts due to the design and fabrication process complexity. It is difficult to understand the trade-offs inherent in the system and achieve an optimal structure without any MEMS-related insight. An attempt is made to develop an integrated systems model for the complete structure of the MEMS product system in terms of its constituents and interactions between the constituents. The hierarchical tree structures of the MEMS system and its subsystems are presented up to component level. For characterization, analysis and identification of MEMS product system, three different mathematical models say graph theoretic model, matrix model and permanent model are presented. These models are associated with graph theory, matrix method and variable permanent function by considering the various subsystems, subsubsystems up to component level, their connectivity and interdependency of the MEMS product system. The developed methodology is explained with an example. The proposed modeling and analysis is extendable to the subsystems and the component level. An overall structural analysis can be carried out by following a 'top-down' approach or 'bottom-up' approach. Understanding of MEMS product structure will help in the improvement of performance, cost, design time, and so on.