Adhesion is important in many industrial applications including those in the microelectronics industry. Flip-chip assemblies commonly utilize epoxy underfills to promote reliability and the buried interfacial structure of underfills is crucial to device lifetime. Poor adhesion at this interface can cause premature device failure. One method to increase adhesion strength is to plasma treat the substrate attached to underfills, however, the mechanism of this increase in adhesion strength has not been thoroughly investigated at the molecular level in situ, because it is difficult to probe a buried interface where the adhesion occurs. In this work, sum frequency generation (SFG) vibrational spectroscopy was utilized to investigate the buried polymer/epoxy resin interface at the molecular level. Plasma treatment was performed on the polymer surfaces and the effects were examined. The buried interfaces between the polymer surface before and after plasma treatment and epoxy were then investigated to understand if the effects of the treatment can be observed using SFG. It was found that the molecular structure of the buried interface of the pristine polymer surface in contact with epoxy is drastically different from the buried interface of the plasma treated surface with epoxy. The buried interface containing the plasma treated polymer surface was found to be considerably more disordered and had much higher adhesion strength. This research elucidates the plasma treatment effects on structures and properties of buried polymer/epoxy interfaces, providing in-depth understanding on the mechanism of adhesion strength increase facilitated by plasma treatment.