A method of removing the residue left after a plasma process is described. First, a substrate having at least a material layer thereon is provided. The material layer includes a metal. Then, a fluorine-containing plasma process is performed so that a residue containing the aforesaid metallic material is formed on the surface of the material layer. After that, a wet cleaning operation is performed using a cleaning agent to remove the residue. The cleaning agent is a solution containing water, a diluted hydrofluoric acid and an acid solution.