During the replication of microstructures in polymers by hot embossing, interfacial forces between the master and polymers need to be reduced by an anti-sticking layer inorder to ensure a clean demolding process. This article presents a comparison of the dodecyltrichlorosilane (DDTS) and perfluorooctyl-1H,1H,2H,2H-trichlorosilane (FTCS) self-assembled monolayer (SAM) in terms of the ultra-thin film property and effectiveness as anti-sticking layers for the micro-structured master. Both type of SAMs have been evaluated in several ways, including atomic force microscopy (AFM), contact angle analysis (CAA), electron microprobe analysis (EPMA) and X-ray photoelectron spectroscopy (XPS). Successful anti-adhesion layer on the master is demonstrated under adequate solution reaction conditions.