Nanostructured fluoropolymer films were deposited via plasma polymerization of allylpentafluorobenzene (APFB) on pristine (native oxide-covered) Si(100) and hydrogen-terminated Si(100) (H-Si) surface. By changing the substrate temperature, radio frequency (RF) power, and system pressure, fluoropolymer films composed of fairly well-defined and uniform nanospheres were deposited. The size and size distribution of the nanospheres in the deposited films was studied by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Under the high RF power (400 W) and high system pressure (800 mTorr), nanoporous fluoropolymer films composed of spheres with mean diameter (D-m) on the order of 120 nm and narrow size distribution (standard deviation in diameter, SD similar to 9 nm) were obtained. The chemical composition and structure of the nanostuctured films were studied by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and Fourier transform infrared (FTIR) spectroscopy. The fluoropolymer films were highly hydrophobic in nature and could give rise to surface water contact angles above 150degrees. Although the morphology of the fluoropolymer films deposited on both types of silicon substrates was similar, chemical interaction at the polymer/H-Si interface had resulted in stronger adhesion of the fluoropolymer film to the silicon substrate.