With the goal of elucidating the structure of polyvinylidene difluoride (PVDF) nanofibers, all-atom molecular dynamics simulations were performed, and the results were compared with structures observed in high resolution transmission electron microscopy (TEM) at the molecular level. Simulation shows that the stability of the b-phase component in a PVDF nanofiber is influenced by the diameter of the nanofiber. In unstretched ultra-thin nanofibers, the b phase is readily transformed into a paraelectric phase. During the TEM imaging process, chain scission due to irradiation can accelerate this process. This transformation illuminates the spindle formation and serpentine motion of molecular segments observed by Zhong et al. (Polymer, 54, 2013, 3745-3756) in irradiated PVDF nanofibers. From a comparison between simulated and experimental TEM images it was possible to identify numerous features that are useful in unveiling inherent structures of PVDF nanofibers. These include the orientations of elongated dots with respect to the chain axis; kinks along the chain profile; varying sizes, shapes, and brightness of dots; and distances between dots. This information allows one to distinguish image of short chain segments having a conformation approximating the a phase from those approximating the b phase. (C) 2017 Elsevier Ltd. All rights reserved.