Water affinity and condensation on Si-based surfaces is investigated to address the problem of fogging on silicone intraocular lenses (IOL) during cataract surgery, using Si(100), silica (SiO2) and polydimethylsiloxane (PDMS) silicone (SiOC2H6)n. Condensation is described by two step nucleation and growth where roughness controls heterogeneous nucleation of droplets followed by Ostwald ripening. Wetting on hydrophilic surfaces consists of continuous aqueous films while hydrophobic surfaces exhibit fogging with discrete droplets. Si-based surfaces with wavelength above 200 nm exhibit fogging during condensation. Below 200 nm, surfaces are found to wet during condensation. Water affinity of Si-based surfaces is quantified via the surface free energy (SFE) using Sessile drop contact angle analysis, the Young-Dupré equation, and Van Oss theory. Topography is analyzed using tapping mode atomic force microscopy (TMAFM). Polymer adsorption and ion beam modification of materials (IBMM) can modify surface topography, composition, and SFE, and alter water affinity of the Si-based surfaces we studied. Wet adsorption of hydroxypropyl methylcellulose (HPMC) C32H60O19 with areal densities ranging from 1018 atom/cm2 to 1019 atom/cm2 characterized via Rutherford backscattering spectrometry (RBS), allows for the substrate to adopt the topography of the HPMC film and its hydrophilic properties. The HPMC surface composition maintains a bulk stoichiometric ratio as confirmed by 4.265 MeV 12C(α, α)12C and 3.045 MeV 16O(α, α)16O, and 2.8 MeV He++ elastic recoil detection (ERD) of hydrogen. Both PIXE and RBS methods give comparable areal density results of polymer films on Si(100), silica, and PDMS silicone substrates. The SFE and topography of PDMS silicone polymers used for IOLs can also be modified by IBMM. IBMM of HPMC cellulose occurs during IBA as well. Damage curves and ERD are shown to characterize surface desorption accurately during IBMM so that ion beam damage can be accounted for during analysis of polymer areal density and composition. IBMM of Si(100)-SiO2 ordered interfaces also induces changes of SFE, as ions disorder surface atoms. The SFE converges for all surfaces, hydrophobic and hydrophilic, as ions alter electrochemical properties of the surface via atomic and electronic displacements.