An apparatus for using hydrodynamic cavitation in medical treatment such as destroying kidney stones or killing infected cancer cells. This apparatus comprises a tank used as a container for a fluid, a compressor connected to the tank to maintain the input pressure of the fluid, a tubing wherein the fluid flows, a probe in which the cavitation occurs, a valve positioned inside the tubing, allowing the fluid to flow into the probe, a filter positioned inside the tubing, preventing the predetermined size particles flowing into the probe, a fitting connecting the probe to the tubing, a flowmeter measuring the volume flow rate of the fluid through the probe, an image capturing unit capturing the sequential images of bubbles growing and bubbles collapsing after the bubbles exit from the probe, a positioning assembly which adjusts the distance between the probe and the target surface, and a control and data acquisition unit.