Capacitive micromachined ultrasonic transducer (CMUT) is a promIsing candidate for making ultrasound transducer arrays for applications such as 3D medical ultrasound, non-destructive evaluation and chemical sensing. Advantages of CMUTs over traditional piezoelectric transducers include low-cost batch fabrication, wide bandwidth, and ability to fabricate arrays with broad operation frequency range and different geometric configurations on a single wafer. When incorporated with throughwafer interconnects, a CMUT array can be directly integrated with a front-end integrated circuit (IC) to achieve compact packaging and to mitigate the effects of the parasitic capacitance from the connection cables. Through-wafer via is the existing interconnect scheme for CMUT arrays, and many other types of micro-electro-mechanical system (MEMS) devices. However, to date, no successful through-wafer via fabrication technique compatible with the wafer bonding method of making CMUT arrays has been demonstrated. The through-wafer via fabrication steps degrade the surface conditions of the wafer, reduce the radius of curvature, thus making it difficult to bond. This work focuses on new through-wafer interconnect techniques that are compatible with common MEMS fabrication techniques, including both surfacemicromachining and direct wafer-to-wafer fusion bonding. In this dissertation, first, a through-wafer via interconnect technique with improved characteristics is presented. Then, two implementations of through-wafer trench isolation are demonstrated. The through-wafer trench methods differ from the through-wafer vias in that the electrical conduction is through the bulk silicon instead of the conductor in the vias. In the first implementation, a carrier wafer is used to provide mechanical support; in the second, mechanical support is provided by a silicon frame structure embedded inside the isolation trenches. Both implementations reduce fabrication complexity compared to the throughwafer via process, and result in low series resistance and small parasitic capacitance. Two-dimensional CMUT arrays incorporating trench-isolated interconnects show high output pressure (2.9 MPa), wide bandwidth (95%), small pulse-echo amplitude variation (sigma = 6.6% of the mean amplitude), and excellent element yield (100% in 16x16-element array). Volumetric ultrasound imaging was demonstrated by flip-chip bonding one of the fabricated 2D arrays to a custom-designed IC. An important added benefit of the trench-isolated interconnect is the capability to realize flexible arrays. A flexible 2D CMUT array is demonstrated by filling the trenches with polydimethylsiloxane (PDMS). The results presented in this dissertation show that through-wafer trench-isolation is a viable solution for providing electrical interconnects to CMUT elements. These techniques are potentially useful for providing through-wafer interconnects to many other types of MEMS sensors and actuators because of their post-process nature. The results also show that 2D CMUT arrays fabricated using wafer-bonding deliver good performance.