Micro- and nanostructures in vapor-phase-grown AlN on face-to-face annealed sputtered AlN (FFA Sp-AlN) templates formed on nanopatterned sapphire substrates (NPSS) were comprehensively analyzed using transmission electron microscopy. The comparison between metal–organic vapor-phase epitaxy-grown AlN/FFA Sp-AlN/hole-type NPSS (Sample MOH) and hydride vapor-phase epitaxy-grown AlN/FFA Sp-AlN/cone-type NPSS (Sample HVC) showed apparent differences in the morphology of dislocation propagation, presence of voids, shape of polarity inversion boundaries, and crystal structure on the slope region of NPSS. Notably, cross-sectional and plan-view observations revealed that the quality of FFA Sp-AlN significantly affects the threading dislocation density in the vapor-phase-grown layer. At the slope region of the AlN/NPSS interface, γ-AlON was observed in the MOH sample, while highly misaligned AlN grains were observed in the HVC sample. These characteristic crystal structures affect the occurrence of dislocations via different mechanisms in each sample. This study provides practical information for strategically controlling the micro- and nanostructures formed in AlN/NPSS structures for high-performance AlGaN-based deep-ultraviolet emitters.