The structural properties and the interaction strength of naphtho[2,3-a]pyrene (NP), a promising multifunctional organic material for optoelectronic devices, has been studied on Au(111) by means of scanning tunnelling microscopy. The perturbation of the native herringbone reconstruction of the pristine Au(111) surface was used to assess the interaction strength of the organic film with the surface. It was found that a moderate temperature treatment (500 K) of the NP film led to a new equilibrium structure, which dramatically perturbed the herringbone reconstruction. Our data suggest that organic-metal interfaces studied at room temperature or lower do not necessarily reflect the true equilibrium structures of the organic films, which are important in understanding the associated properties of organic thin film electronic devices. Interpretation of the self-assembled NP structure on Au(111) is discussed in conjunction with STM tip induced imaging effects which appear prevalent on these complex organic/metal interfaces.