In one embodiment, an apparatus of treating a surface of a semiconductor substrate comprises a substrate holding and rotating unit, first to fourth supplying units, and a removing unit. A substrate holding and rotating unit holds a semiconductor substrate, having a convex pattern formed on its surface, and rotates the semiconductor substrate. A first supplying unit supplies a chemical onto the surface of the semiconductor substrate in order to clean the semiconductor substrate. A second supplying unit supplies pure water to the surface of the semiconductor substrate in order to rinse the semiconductor substrate. A third supplying unit supplies a water repellent agent to the surface of the semiconductor substrate in order to form a water repellent protective film onto the surface of the convex pattern. A fourth supplying unit supplies alcohol, which is diluted with pure water, or acid water to the surface of the semiconductor substrate in order to rinse the semiconductor substrate. A removing unit removes the water repellent protective film with the convex pattern being left.