When thin films are deposited from plasma with a significant a degree of ionization or under ion bombardment, the energy of the incident ions can be used as an effective means for engineering microstructures. Ion energy has been increasingly used as a deposition parameter. The introduction of plasma immersion ion implantation has made ion-assisted processes more amenable for industrial implementation because it has diminished the complexity of hardware, and allowed larger areas and complex shapes to be treated. Here we discuss the impact of energetic particles on the microstructure and properties of films produced by filtered cathodic arc (FCA) and magnetron sputter (MS) deposition with ion assist. Amorphous hard carbon films with high content of sp3-hybridization were prepared using both techniques under optimum ion bombardment conditions to maximize the content of tetrahedral-bonded carbon. Techniques for controlling film properties by altering the nano-structure are presented. The effect of energetic particles on conventional and sculptured thin-films is also discussed and examples of metallic and ceramic films are presented and discussed in light of atomic mechanisms.