This article presents an innovative model-based scatterometry method for CD metrology of single high-aspect-ratio (HAR) microstructures, which are increasingly utilized in advanced packaging, especially as vertical interconnects in three-dimensional integrated circuits. The rapidly growing aspect ratio of these HAR structures makes it challenging to monitor their critical dimensions (CD). Furthermore, conventional spectral reflectometry or scatterometry measurements on periodic metrology targets on the scribe lines of the wafer are inadequate in providing a reliable correlation with the in-die structures due to the integral nature of these measurements, which can result in additional measurement errors compared to measuring individual in-die structures. To address these challenges, we propose a novel scatterometry system that can achieve high-precision single-structure measurement of fine-pitch HAR structures with significantly improved light efficiency over conventional optical methods. Our system takes advantage of the high spatial coherence of the supercontinuum laser source and an optical NA-controlled design concept for precise light beam shaping, enabling high spatial resolution and superior light efficiency in measurements. Furthermore, we demonstrate a model-based measurement scheme that uses a virtual optical system for complete characterization of the sample profile. The experimental results show that the proposed system can accurately measure RDL structures with fine nominal spacing as small as 1 μm and an aspect ratio of 3:1 with high fidelity.