Though 3D TSV/TSI technology provides the promising platform for heterogeneous system integration with design drivers ranged from thousand-core microprocessor to millimeter-cubic sensor, the fundamental challenge is lack of light to deal with significantly increased design complexity. From device level, new state of variables from different physical domains such as MEMS, microfluidic and NVM devices have to be identified and described together with conventional states from CMOS VLSI; and from system level, cyber management of states of voltage-level and temperature has to be maintained under a real-time demand response fashion. Moreover, a cyber-physical link is required to compress and virtualize device level state details during system level state control. This paper shows device-level 3D integration by example of MEMS and CMOS VLSI. In addition, a cyber-physical thermal management for 3D integrated many-core microprocessors is discussed.