Poly (dimethylsiloxane) (PDMS) is meant to be utilized for a miniaturized sensor system. However, protein and biospecies often adsorb onto a PDMS surface nonspecifically. This matter is a serious challenge in the study of miniaturized sensor systems. We provide the solution, which is a prevention technique of nonspecific adsorption onto a PDMS microchip by using a functionalized silane compound self-assembled monolayer. Two demonstrations for bacteria and explosives were examined by atomic force microscopy and x-ray photoelectron spectroscopy. It was found that 1H, 1H, 2H, 2H-Perfluorooctyltriethoxysilane self-assembled monolayer on PDMS effectively blocked the nonspecific adsorption of Escherichia coli (O157:H7) and explosives such as 2, 4, 6-trinitrotoluene and 1, 3, 5-trinitroperhydro-1,3,5-triazine (RDX, Research Department Explosive).