The use of proteins and peptides to deposit and pattern metallic nanoparticles is becoming increasingly important. This method provides an inexpensive procedure to produced patterned and continuous metallic nanoparticles on variety of substrates such as silicon dioxide, silicon nitride, and polyimide. In this work, we explore the use of proteins and peptides for patterning and depositing gold nanoparticles. We used two different peptides or proteins for this experiment. One is 3XFLAG peptide from Sigma-Aldrich and the other one is bovine serum albumin (BSA). To pattern the peptides on the substrates we used two different methods, photolithography and micro-transfer molding. In photolithography, S1813 photoresist was patterned on the substrates through clean room process. In the micro-transfer molding process, a PDMS mold was made out of photoresist pattern. Polypropylmethacrylate (PPMA) was spin coated on the PDMS mold and stamped on the substrate in a high temperature. The proteins were adsorbed on the surface either physically or covalently. To deposit gold nanoparticles, the substrates with adsorbed proteins were covered with aqueous HAuCl4 solution. The proteins catalyze gold nanoparticles reduction from the solution. To characterize nanoparticles we used SEM and Electron Beam Induced Current (EBIC).