The influence of silicon surface damage on nickel-silicide (NiSi) has been characterized and H$_2$ anneal and TiN rapping has been applied to suppress the electrical, morphological deterioration phenomenon incurred by the surface damage. The substrate surface is intentionally damaged using Ar IBE (Ion beam etching) which can Precisely control the etch depth. The sheet resistance of NiSi increased about 18% by the surface damage, which is proven to be mainly due to the reduced silicide thickness. It is shown that simultaneous application of H: anneal and TiN capping layer is highly effective in suppressing the surface damage effect.