The reaction of an atomic beam of O(P-3) with organized organic thin films (OOTFs) of amphiphilic molecules was investigated applying in-situ IR, XPS, and wettability measurements. Both kinetics and surface temperature effects were monitored. The reaction probability was much larger for the OOTF relative to the gas phase process. The reaction rate was found to depend on the organization of the thin films. Structural phase transition was observed by monitoring the changes in reactivity. A curve-crossing model explains the observations and rationalizes the lack of activation energy and the dependence of the reactivity on the penetrability in between the chains.