Cold temperature atmospheric pressure plasma (APP) produces many types of chemically reactive species and is capable of modifying materials at atmospheric pressure. Studying plasma-surface interaction (PSI) at such pressure has been challenging due to the small mean-free-path (< 100 nm) which prohibits the conventional method of using independently controlled beams of ions/neutrals to isolate the role of each species. In this dissertation, we developed an alternative approach of studying PSI at atmospheric pressure using well-controlled source-ambient-sample systems and comprehensive surface/gas phase characterization techniques. In this new approach, we emphasize the controlled generation of reactive species from the plasma source, the regulated transportation of reactive species to the target surfaces, as well as the simplified material structure subjected to plasma treatment. To isolate and identify the role of certain reactive species on materials, a plasma source is selected with its operating conditions carefully tuned for the delivery of such species to target surface. Plasma-induced effects on model polymers and biomolecules were characterized and then quantitatively correlated to the gas phase species. Due to the multi-phase nature of PSI, many characterization techniques, including that of plasma/gas phases such as optical emission spectroscopy (OES), Fourier transform infrared spectroscopy (FTIR) and UV absorption, and that of material surfaces such as X-ray photoelectron spectroscopy (XPS), attenuated total reflection (ATR) FTIR and Ellipsometry were adopted. Using this approach, we were able to evaluate the effect of both short- and long-lived reactive neutrals on many types of surface moieties. For example, we find that atomic O and OH radicals are able to cause fast material removal but moderate oxidation on the etched surface. We also find that O3 can participate in the chemical modification of aromatic rings, i.e. cleavage and their conversion into ether, ester carbonyls and surface organic nitrate groups, both on surface and in the polymer bulk. We also find evidence for (1) the competition between etching and surface modification processes when a high density of short-lived reactive species is involved, and (2) three polymer transformation stages when large fluxes of long-lived reactive species are interacting with styrene-based polymers. Lastly, we extended our work to explore the potential application of APP reactors for disinfecting raw foods and evaluated bacterial inactivation mechanisms.