Abstract: A method of manufacturing a semiconductor device such as a contact structure and a gate structure having a silicide layer comprises the steps of: forming a contact hole for exposing a part of the silicon substrate by etching a part of an interdielectric layer formed on a silicon substrate; and first cleaning an exposed surface of the silicon substrate, comprising the steps of: forming a reactive layer by supplying a hydrogen gas in a plasma state and a fluorine-series gas to the silicon substrate and by chemically reacting with an oxide film formed on the exposed surface of the silicon substrate; and annealing to cause the reactive layer to be removed by vaporizing the reactive layer; forming a silicide layer on the surface of the silicon substrate exposed in the contact hole; second cleaning comprising the steps of: forming a reactive layer by supplying a hydrogen gas in a plasma state and a fluorine-series gas to the silicon substrate and by chemically reacting with an oxide film formed on the exposed surfa