In a method of cleaning a bottom of a via hole, a copper oxide on a surface of an underlying Cu wiring exposed at the bottom of the via hole is removed before forming a Cu wiring in a trench and the via hole extended between the trench and the underlying Cu wiring. The trench and the via hole are formed in a predetermined pattern in an interlayer insulating film of a substrate. Reducing species containing a metal in a state capable of reducing the copper oxide is supplied to the bottom of the via hole. The metal has a higher oxidation tendency than Cu and an oxide of the metal has a lower electrical resistance than the copper oxide. The copper oxide is removed by reducing the copper oxide and the oxide of the metal is generated through a reaction between the metal in the reducing species and the copper oxide.