3Dimensional Integration can solve many challenges which are being faced by modern planer integration. The major bottleneck of 3D-Integration are contamination and Copper surface oxidation which is the cause of the requirement of high temperature while bonding. Reduction of this high bonding temperature is the key challenge of 3Dimensional Integration. In this research work we investigate and compare the Copper surface protection characteristic of Self Assembled Monolayer(SAM) of Alkyl Thiol having different Carbon chains(C6,Hexanethiol and C12, Dodecanethiol). We also study the thermal desorption of these SAM layers. SAM can minimize the oxidation of the Copper which acts as a bonding medium. By thermal desorption the pure Copper surface is brought back and exposed. Finally Copper-Copper thermocompression bonding is performed in different conditions and compared. © (2013) Trans Tech Publications, Switzerland.