Ultrafast non-diffractive Bessel laser beams provide strong light confinement and show robust advantages for fabricating high-aspect-ratio nanoscale structures inside transparent materials. They take the form of nanoscale voids with typical diameters well below the wavelength and aspect ratio of more than 1000. Delivering 3D morphologies of such nanoscale voids is an important issue to evaluate the result for fabrication. However, the characterization of such laser-induced structures is a difficult task. Here, an accurate and time-saving tomography-like methodology is proposed and adopted for reconstructing the morphology of high-aspect-ratio nano-holes. The technique allows an accurate assertion of laser parameters and position on nano-structured features. The reconstructed configuration reveals that nanoholes morphologies have a close relationship with energy distribution in the focal region. It suggests that the configuration of micro-explosion can be controlled by laser energy deposition in the process of laser-matter interaction down to the nanoscale. © 2020 by the authors.