Study of wetting and nonwetting surfaces is very significant in various fields of science. Stability of selfassembled wettable layers over any surface is vital in that respect. The generation and then detection of defect sites on such surfaces is also ominously important. In this study, self-assembled monolayers of PFDTS (1H,1H,2H,2H perfluorodecyltrichlorosilane) molecules on silicon-wafer have been created by vapour deposition method. Due to fluorinated tail of PFDTS molecule, the nature of surface will become hydrophobic. Such hydrophobic surface normally leaves no deposits, except at a single point over the surface. Defect sights on PFDTS region produces confined areas on the hydrophobic surface with different wettability. Such sights will facilitate narrowed deposition ofnanoparticles within the hydrophobic defects. These fluidic deposits will facilitate nanoscale interactions and drying capillaries to play their role within such regions. Hydrophobic regions without defects show clean surface with no deposition of nanoparticles, whereas close-packed gold nanorods have been observed within the confined defect regions on PFDTS.