The methods and systems disclosed here detect edges of top-down images of respective cross-sections of an array of high-aspect-ratio (HAR) features. The respective cross sections are at various depths of a HAR feature along a longitudinal direction. The detected edges are re-sampled in a spatial domain at a target angular resolution. The re-sampled edges are represented as a corresponding set of harmonics in a frequency domain, each set of harmonics preserving characteristic information about a respective cross-section of the HAR feature at a certain depth. A plurality of cross-sections at the various depths of the HAR feature are reconstructed by analyzing the corresponding sets of harmonics in the frequency domain. A 3D profile of the HAR feature is generated by stitching the plurality of re-constructed cross-sections at the various depths of the HAR feature.