Energetic ions in a plasma can be used for synthesis, modification and removal of materials on a micrometer to nanometer size scale. One technique that uses this approach is the Plasma Immersion Ion Implantation and Deposition (PIIID) technique which can be used either for the intrinsic modification of the chemistry and microstructure of the near-surface regions of a material or for the deposition of overlay films on surfaces of materials. The ability to alter the ion energy over a wide range in PIIID can be used for “atomic stitching” to enhance film-substrate adhesion. It can also be used to alter the near-surface chemistry of the a multi-component alloys by utilizing differential sputtering effects, for plasma cleaning, and for hardening polymeric thin films by cross-linking and other conversion mechanisms. The presentation will cover structural changes in materials during the PIIID processing and various applications of this technology.