A method and an apparatus for cleaning semiconductor devices, in which water droplets are completely eliminated after the wafer is cleaned in the course of the semiconductor manufacturing process. In the method and apparatus, after the thin film is cleaned, a cut off valve cuts off the supply of cleaning solution to a cleaning container. At the same time, a first drain valve, second drain valve, and third drain valve respectively open a first drain path, a second drain path, and third drain path in serial order, with a predetermined time interval between each stage, thereby slowly draining the cleaning solution from the container. The cleaning solution is easily and nearly completely separated from the wafer due to the surface tension of the cleaning solution, and no large drops of the cleaning solution are left on the wafer.