A system and method for determining clearance between a fabrication tool and a workpiece is provided. In an exemplary embodiment, the method includes receiving a substrate within a tool such that a gap is defined there between. A transducer disposed on a bottom surface of the substrate opposite the gap provides an acoustic signal that is conducted through the substrate. The transducer also receives a first echo from a top surface of the substrate that defines the gap and a second echo from a bottom surface of the tool that further defines the gap. A width of the gap is measured based on the first echo and the second echo. In some embodiments, the bottom surface of the tool is a bottom surface of a nozzle, and the nozzle provides a liquid or a gas in the gap while the transducer is receiving the first and second echoes.