Polyatomic ions with collision energies from 5 - 200 eV can be used to deposit films and modify surfaces in a highly controllable fashion. Low energy polyatomic ions are very surface selective, interact with surfaces via a unique collision dynamics, and can be used to transfer part or all of their chemical functionality to a surface. Ionization and mass-selection permits the facile preparation of a wide range of reactive species. Collision energy can be further used to control the final film properties. Examples discussed will include the deposition of 1) cross-linked fluorocarbon films on polystyrene by 25 - 100 eV CF@sub 3@@super +@ and C@sub 3@F@sub 5@@super +@ and 2) cross-linked organosiloxane films on Al by 15 - 100 eV Si@sub 2@O(CH@sub 3@)@sub 5@@super +@. Monochromatic x-ray photoelectron spectroscopy and contact angle measurements are used to determine film chemistry. Atomic force microscopy and x-ray reflectivity are used to determine film thickness and morphology. Oxidation and other aging processes are also examined for these films following air exposure for several weeks. Molecular dynamics simulations support the experimental results and compare the surface interaction process for different ion isomers. These results show that the size and structure of the depositing ion affects film formation via different chemical structure, reactivity, sticking probabilities, and energy transfer to the surface. These results also indicate that polyatomic ions and energetic neutrals likely play an important role in film deposition and surface modification during plasma polymerization, laser ablation of polymers, and sputter deposition of polymers.