Three-dimensional (3D) flow reconstruction over a 6:1 prolate spheroid using scanning stereoscopic particle image velocimetry has been conducted in a towing-tank facility. Forces, moments, surface pressure and reconstructed 3D vortical-flow structures are acquired in order to characterize the separated flow within the subcritical regime at three Reynolds numbers (Re = 0.5 × 106, 1.0 × 106 and 1.5 × 106), and at four incidence angles (α = 5◦, 10◦, 15◦ and 20◦). Key flow features are evaluated through the reconstructed 3D flowfield data. In particular, the interaction of the crossflow vortices and the surface-pressure distribution are discussed. It is shown that the crossflow vortices consist of helical vortex tubes as the dominant coherent structures, which are more distinct at large α. For α ≥ 15◦, four high-vorticity regions were observed. A pair of upper vortex tubes, originate on the windward side of the model, while a lower vortex tube is formed on the strong curvature region on the leeward side of the model. The vortex dynamics are further characterized through stretching and tilting terms via the vorticity-transport equation. Larger incidence angles α lead to a stronger alignment of the crossflow vortices with the mean flow direction, which is reflected in the tilting terms. A weak Re dependency of the loads and flow structures within the range 1.0 × 106 ≤ Re ≤ 1.5 × 106 is reported, while a significantly different result was captured for separation at Re = 0.5 × 106. An increase in separation size at Re = 0.5 × 106 at 20◦ results in an additional flow structure; a pair of secondary vortices is formed, leading to a change in the pressure distribution on the model surface when compared to higher Re.