A method as disclosed makes a capacitive micromachined ultrasonic transducer (cMUT). The method forms a pattern of standing features on a substrate to serve as support walls in the cMUT being made, and further makes a patterned trench from the front side into the substrate at selected locations where separation boundaries of neighboring elements of the cMUT are located. In the process of completing the transducer elements of the cMUT, the method forms a covering layer over the patterned trench to at least temporarily cover the patterned trench. The covering layer seals the patterned trench to prevent other materials from entering during at least a part of the fabrication process.