In the present paper, the deposition processes and formation of films in SF6 ion-ion plasma, with positive and negative ion flows accelerated to the surface, are investigated. The PEGASES (acronym for Plasma Propulsion with Electronegative GASES) source is used as an ion-ion plasma source capable of generating almost ideal ion-ion plasma with negative ion to electron density ratio more than 2500. It is shown that film deposition in SF6 ion-ion plasma is very sensitive to the polarity of the incoming ions. The effect is observed for Cu, W, and Pt materials. The films formed on Cu electrodes during negative and positive ion assisted deposition were analyzed. Scanning electron microscope analysis has shown that both positive and negative ion fluxes influence the copper surface and leads to film formation, but with different structures of the surface: the low-energy positive ion bombardment causes the formation of a nano-pored film transparent for ions, while the negative ion bombardment leads to a continuous smooth insulating film. The transversal size of the pores in the porous film varies in the range 50–500 nm, and further analysis of the film has shown that the film forms a diode together with the substrate preventing positive charge drain, and positive ions are neutralized by passing through the nano-pores. The film obtained with the negative ion bombardment has an insulating surface, but probably with a multi-layer structure: destroying the top surface layer allows to measure similar “diode” IV-characteristics as for the nano-pored film case. Basing on results, practical conclusions for the probes and electrodes cleaning in ion-ion SF6 plasmas have been made. Different applications are proposed for the discovered features of the controlled deposition from ion-ion plasmas, from Li-sulphur rechargeable batteries manufacturing and nanofluidics issues to the applications for microelectronics, including low-k materials formation.