Thin films of light atomic weight elements in amorphous, partially-crystalline, or crystalline forms have applications in a broad range of technologies. For example, amorphous tetrahedral carbon (a-tC) and polymeric thin films impact electronic materials technology as electron- and light-emitting device elements, respectively. A lack of crystallinity introduces complexity in the experimental and theoretical characterization of these materials but is not necessarily a limiting factor in their performance. While the growth process is clearly a major factor governing the physical properties of a film, interactions with the substrate are also important, so surface and interface analysis provides an important complement to bulk measurements. Currently, the fundamental and applied aspects of the atomic, electronic and vibrational structure of these complex materials are being elucidated by novel approaches combining several experimental techniques with theoretical calculations. This paper focuses on several approaches in the characterization and modification of thin films made possible by recent experimental advances. The structural and electronic properties of two model systems are considered as examples: a-tC thin films grown by pulsed laser deposition (PLD) and poly aniline thin films grown by vapor deposition. First, scanning probe microscopies and x-ray scattering are used to investigate the structural aspects of a-tC films as a function of PLD growth conditions. The possible connection of nanoscale surface modification and characterization with electron emission properties will be discussed. Second, the results of inelastic scattering spectroscopy and other surface techniques will be discussed to obtain information on both interfacial aspects of the growth of polyaniline thin films and microscopic and macroscopic aspects of electrical conductivity upon doping. Comparisons will be made with other studies that address properties of analogous crystalline systems as appropriate. A brief assessment of the broader problem of analyzing these systems will be given.