Polyatomic ions can be used to deposit thin films, modify the phases of interfaces, dope trace elements into interface regions, impact specific chemical functionalities to a surface, and create micron- and nanometer-scale interface structures. This article demonstrates the broad flexibility over the modified surface properties allowed by variation of the incident ion chemical structure and kinetic energy. Organosiloxane (OS) films are deposited here on Al from mass-selected 15-100 eV Si2O(CH3)(5)(+) ions. Monochromatic x-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry are used to determine the OS film chemistry. The OS films vary from essentially organic (lightly cross-linked network) at 15 eV deposition to a more inorganic (highly cross-linked "silica like") at 100 eV. XPS is also used to examine the aging of fluorocarbon films deposited on polystyrene by 25-100 eV CF3+ and C3F5+ ions. These films undergo only minor changes during aging, forming only a few percent oxygen on the surface. Surface restructuring and other processes are also observed in these fluorocarbon films during aging for up to 8 weeks.