We report a novel approach to reconstruct the cross-sectional profile of fabricated hollow-core photonic bandgap fibers from scanning electron microscope images. Finite element simulations on the reconstructed geometries achieve a remarkable match with the measured transmission window, surface mode position and attenuation. The agreement between estimated scattering loss from surface roughness and measured loss values indicates that structural distortions, in particular the uneven distribution of glass across the thin silica struts on the core boundary, have a strong impact on the loss. This provides insight into the differences between idealized models and fabricated fibers, which could be key to further fiber loss reduction.