We have designed, fabricated, and characterized two-dimensional 16x16-element capacitive micromachined ultrasonic transducer (CMUT) arrays. The CMUT array elements have a 250-μm pitch, and when tested in immersion, have a 5 MHz center frequency and 99% fractional bandwidth. The fabrication process is based on standard silicon micromachining techniques and therefore has the advantages of high yield, low cost, and ease of integration. The transducers have a Si3N4 membrane and are fabricated on a 400-μm thick silicon substrate. A low parasitic capacitance through-wafer via connects each CMUT element to a flip-chip bond pad on the back side of the wafer. Each through wafer via is 20 μm in diameter and 400 μm deep. The interconnects form metal-insulator-semiconductor (MIS) junctions with the surrounding high-resistivity silicon substrate to establish isolation and to reduce parasitic capacitance. Each through-wafer via has less than 0.06 pF of parasitic capacitance. We have investigated a Au-In flip-chip bonding process to connect the 2D CMUT array to a custom integrated circuit (IC) with transmit and receive electronics. To develop this process, we fabricated fanout structures on silicon, and flip-chip bonded these test dies to a flat surface coated with gold. The average series resistance per bump is about 3 Ohms, and 100% yield is obtained for a total of 30 bumps.