Birds primarily create and control the forces necessary for flight through changing the shape and orientation of their wings and tail. Their wing geometry is characterised by complex variation in parameters such as camber, twist, sweep and dihedral. To characterise this complexity, a multi-view stereo-photogrammetry setup was developed for accurately measuring surface geometry in high resolution during free flight. The natural patterning of the birds was used as the basis for phase correlation-based image matching, allowing indoor or outdoor use while being non-intrusive for the birds. The accuracy of the method was quantified and shown to be sufficient for characterising the geometric parameters of interest, but with a reduction in accuracy close to the wing edge and in some localised regions. To demonstrate the method's utility, surface reconstructions are presented for a barn owl (Tyto alba) and peregrine falcon (Falco peregrinus) during three instants of gliding flight per bird. The barn owl flew with a consistent geometry, with positive wing camber and longitudinal anhedral. Based on flight dynamics theory, this suggests it was longitudinally statically unstable during these flights. The peregrine falcon flew with a consistent glide angle, but at a range of air speeds with varying geometry. Unlike the barn owl, its glide configuration did not provide a clear indication of longitudinal static stability/instability. Aspects of the geometries adopted by both birds appeared to be related to control corrections and this method would be well suited for future investigations in this area, as well as for other quantitative studies into avian flight dynamics.