Method and apparatus for removing bubbles from a molten substrate. The molten substrate from a furnace passes through a downtube to reach additional manufacturing tools, such as an extrusion bushing. One or more ultrasonic sensors are arranged along the downtube. The ultrasonic sensor(s) transmit ultrasonic energy into the molten substrate and measure a characteristic of the ultrasonic energy, such as a propagation time for the ultrasonic energy to be reflected back to the ultrasonic sensor(s). A bubble is detected when a change in the characteristic of the ultrasonic energy is detected. When a bubble is detected, flow through the downtube is diverted to a duct to remove a slug of molten substrate that includes the bubble.