The influence of process conditions on the structural hierarchy developed in the heat-affected zone (HAZ) of polyethylene 2,6-naphthalene dicarboxylate (PEN) welded both from amorphous, as well as crystalline, precursors was studied using optical microscopy and a matrixing microbeam X-ray diffraction camera developed in our laboratories. The structural gradients developed in the HAZ were found to be highly dependent on welding conditions as well as on the state of crystallinity in the precursor samples. In the amorphous sample, the HAZ is composed of 2 distinct layers. The inner layer (II) (HAZ-II) is formed at the immediate vicinity of the original weld interface, and, within this region, the sample is highly oriented and crystallized. In the outer layer (I) (HAZ I), between this layer and the unaffected region, the polymer exhibit deformed zones, but little or no crystallinity is noticed. In HAZ-I, the polymer chains melt and deform significantly and crystallize upon cooling; and in the HAZ I, the polymer chains located in this region increase their temperature to reach temperatures T > T-g, where they are deformed under the dynamic forces generated at the weld interface as well as under the normal forces. Due to the low crystallizability of PEN chains, the material mostly remain amorphous at this location. In the HAZ, a wave-like interface was observed at the bothe HAZ-II and HAZ I boundaries. This was attributed to the presence of 2 regions of deformable bodies of large difference in viscosities which, in the presence of oscillatory stress field, results in wavy interface. The structural analysis revealed that as a result of significant shearing, the naphthalene planes are oriented parallel to the weld interface resembling graphitic structure. This had a detrimental effect on the mechanical performance of the parts, particularly in those samples welded from amorphous precursors. The samples welded from crystalline precursors exhibited more traditional HAZ structure gradient, and the boundary between the heat-affected and unaffected region is rather diffuse reflecting the rather broad nature of the melting temperature range in this polymer due to dynamic temperature gradient developed during and after the vibration stage.