Three-dimensional (3D) imaging of nanostructures with high aspect ratio features is a challenging problem of broad relevance to nanoscience and nanotechnology. Though a wide variety of experimental strategies to improve 3D imaging capabilities have been proposed, current measurement capabilities are mainly limited to imaging deep trenches, in large part due to the lack of truly 3D scanning algorithms and limited dynamic control of the fill angle. Herein, we report a non-contact atomic force microscope (AFM) strategy that overcomes these challenges by employing an intelligent 3D scanning algorithm that combines sidewall detection and real-time adjustment of the probe's direction. To test this approach, we measured the depth and sidewall topography of porous anodic aluminum oxide (trench), via holes and silicon nanopillar (protrusion) with precision tracing. Using a carbon nanotube-based AFM probe, it was possible to measure the depth of holes with an aspect ratio of 5.9. In addition to this, we have successfully achieved the 3D image of via holes with an aspect ratio of 4.3 and a resolution of 2 nm, which enables realistic profiling of the sidewall and bottom edge of holes. Taken together, our findings demonstrate how the intelligent scanning algorithm based on detection-and-decision with a high-aspect-ratio probe can be utilized as a broadly applicable nanoscience measurement tool to characterize 3D topographical features of nanostructures.