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A novel automated carbon nanotube (CNT) microinjection system for batch fabricated bulk multiwalled carbon nanotubes (MWNT) based MEMS sensor is presented. The basic process includes AC electrophoretic manipulation of MWNT bundles on a silicon substrate and embedding them inside parylene C layers to provide a robust protection for the bundled MWNT. By utilizing AC electrophoretic technology, CNTs were successfully and repeatedly manipulated between micro-fabricated electrodes. Besides, the devices were demonstrated to potentially serve as novel thermal sensors with low power consumption (∼ μW) and fast frequency response (∼ 100 kHz). Based on these experimental evidences, a feasible batch manufacturable method for functional CNT sensors by using the automated injection system is developed which will dramatically reduce production costs and production time of nanosensing devices and potentially enable fully automated assembly of CNT based devices.