The chemically distinctive domains of mixed self-assembled monolayers (SAMs) were investigated by lateral force microscopy (LFM). Mixed SAMs were formed onto the silver coated Si-wafers by soaking them into the ethanolic solution of 11-aminoundecanoic acid (H2(N)(CH2)(10)COOH) and undecanoic acid (CH3(CH2)(9)COOH). Based on the LFM images, it was found that the distinctive domains were formed due to the different functional groups. The prepared mixed SAMs were used as a template for the adsorpton of bacteriorhodops in (bR). It is concluded that site-directed adsorption of the protein molecules would he possible by using the mixed SAMs containing different functional groups.