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This paper presents a deep reactive-ion etching (DRIE)-based post-CMOS micromachining process that provides robust electrically isolated single-crystal silicon (SCS) microstructures for integrated inertial sensors. Several process issues arise from previously reported three-axis CMOS microelectromechanical system (MEMS) accelerometers, including sidewall contaminations of SCS microstructures in plasma etch and a severe silicon undercut caused by overheating of suspended microstructures. Solutions to these issues have been found and are discussed in detail in this paper. In particular, a lumped-element model is developed to estimate the temperature rise on suspended microstructures in a silicon DRIE process. Based on the thermal modeling and experiments, a thick photoresist layer has been used as a thermal path to avoid the severe silicon undercut. The sidewall contamination problem is also eliminated using the modified CMOS-MEMS process. A three-axis accelerometer with a low-noise, low-power on-chip amplifier has been successfully fabricated using the new process. Footing effect was observed on the backside of the sensor microstructure, but it has little effect on the structural integrity and sensitivity of the sensor.