Photochemical patterning of self-assembled mono layers (SAMs) has been performed by diode pumped solid state (DPSS) 3rd harmonic Nd:$YVO_4$ laser with wavelength of 355 nm. SAMs patternings of parallel lines have subsequently been used either to generate compositional chemical patterns or fabricate microstructures by a wet etching. This paper describes a selective etching process with patterned SAMs of alkanetiolate molecules on the surface of gold. SAMs formed by the adsorption of alkanethiols onto gold substrate employs as very thin photoresists. In this paper, the influence of the interaction between the functional group of SAMs and the etching solution is studied with optimal laser irradiation conditions. The results show that hydrophobic functional groups of SAMs are more effective for selective chemical etching than the hydrophilic ones.