In this paper SAM (self-assembled monolayers) is used to passivate cobalt microbumps for 3D-stacking of Si chips. The SAM deposition process is optimized, using input from characterization techniques such as water contact angle measurement, ATR, AFM and XPS analysis in order to form a monolayer of Thiols-SAM on cobalt microbumps. A 3D stacked Si chips test vehicle was used to demonstrate the effectiveness of the SAM coating on cobalt bumps by measuring the electrical continuity of daisy chains.