An atmospheric pressure plasma jet (APPJ) was used to treat polystyrene (PS) films under remote conditions where neither the plume nor visible afterglow interacts with the film surface. Carefully controlled conditions were achieved by mounting the APPJ inside a vacuum chamber interfaced to a UHV surface analysis system. PS was chosen as a model system as it contains neither oxygen nor nitrogen, has been extensively studied, and provides insight into how the aromatic structures widespread in biological systems are modified by atmospheric plasma. These remote treatments cause negligible etching and surface roughening, which is promising for treatment of sensitive materials. The surface chemistry was measured by X-ray photoelectron spectroscopy to evaluate how ambient chemistry, feed gas chemistry, and plasma-ambient interaction impact the formation of specific moieties. A variety of oxidized carbon species and low concentrations of NOx species were measured after APPJ treatment. In the remote conditions used in this work, modifications are not attributed to short-lived species, e.g., O atoms. It was found that O3 does not correlate with modifications, suggesting that other long-lived species such as singlet delta oxygen or NOx are important. Indeed, surface-bound NO3 was observed after treatment, which must originate from gas phase NOx as neither N nor O are found in the pristine film. By varying the ambient and feed gas chemistry to produce O-rich and O-poor conditions, a possible correlation between the oxygen and nitrogen composition was established. When oxygen is present in the feed gas or ambient, high levels of oxidation with low concentrations of NO3 on the surface were observed. For O-poor conditions, NO and NO2 were measured, suggesting that these species contribute to the oxidation process, but are easily oxidized when oxygen is present. That is, surface oxidation limits and competes with surface nitridation. Overall, surface oxidation takes place easily, but nitridation only occurs under specific conditions with the overall nitrogen content never exceeding 3%. Possible mechanisms for these processes are discussed. This work demonstrates the need to control plasma-ambient interactions and indicates a potential to take advantage of plasma-ambient interactions to fine-tune the reactive species output of APP sources, which is required for specialized applications, including polymer surface modifications and plasma medicine.