Electro-optical (EO) systems have wide range of applications and in recent years, especially the use of EO imaging systems in military and civil aviation applications have substantially increased. In these applications, EO systems are exposed to quite harsh and unstable operating conditions like sudden changes in temperature and humidity, dust, fog, physical shock, vibration and radiation. If their optical surfaces such as prisms, lenses and mirrors are damaged due to these conditions, their repair usually is not possible. To overcome these problems, it is necessary to develop special protective coating layers for optical surfaces. The main goal of this study is to produce protective, self-cleaning and super-hydrophobic polymeric thin films for optical surfaces of the electro-optical (EO) systems. Initiated chemical vapor deposition (iCVD) is a novel method for the fabrication of thin film coatings and it has many advantages such as low production cost, very low deposition temperature, 3D geometry coating performance and high deposition rate. Therefore, iCVD was employed to fabricate homopolymers of poly (glycidyl methacrylate) (PGMA) and poly (1H, 1H, 2H, 2H-Perfluorodecyl acrylate) (PPFDA) and P(GMA-PFDA) copolymer thin-films as protective coatings for EO systems. Optical modeling and simulations were performed to determine the effect of film thickness and refractive index on optical performance of substrates to be coated. Optical performance of fabricated coatings was also measured between 400 and 1000 nm range to confirm that protective coatings do not have any measureable impact on optical performance provided that the protective film thickness is kept between 50 nm to 1 μm. The surface morphology of the protective coatings was evaluated using a variety of analytical tools such as Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and Contact Angle measurements. Optical tests were performed by following MIL-F-48616 Military Standard (MIL-STD). The best protective coatings were obtained by using P(GMA-PFDA) copolymer which yields good mechanical properties due to epoxy pendant group and super hydrophobicity due to incorporation of fluoro monomer.