Method of manufacturing a semiconductor device having a silicide layer

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 surface of the silicide layer; and annealing to cause the reactive layer to be removed by vaporizing the reactive layer; and charging a metal layer in the contact hole, in which the silicide layer is formed. In case of the gate structure, the cleaning processes are performed by the same principle before and after forming the silicide layer on a gate electrode material. Accordingly, according to the present invention, the underlying layer of a native oxide film is not damaged or contaminated, and an effective cleaning is performed, thereby improving the reliability of the semiconductor device.