A method of cleaning polycide gates after an etching step. A gate oxide layer, a polysilicon layer, a titanium nitride layer, a silicide layer, an anti-reflection layer and a patterned photoresist layer are sequentially formed over a substrate. An etching operation is next carried out to form a gate structure. The gate structure is formed by patterning the polysilicon layer, the titanium nitride layer and the silicide layer. The gate structure is subsequently cleaned in a three-step cleaning operation. In the first cleaning step, minute amount of fluoride-containing compound, hydrogen and inert gas are used as gaseous reactants in a plasma-cleaning operation. The fluoride-containing compound is capable of initiating a free radical chain reaction. In the second cleaning step, a solvent containing ammonium ions is applied to the gate structure. In the third cleaning step, a solution formed by dissolving oxidizing agent in de-ionized water is applied.