Electron tomography and image analysis are combined to characterize ordered mesoporous silica SBA-15. The morphology of the mesopores with average diameter 6 nm is analyzed in terms of cylinders having variable radii and centers that are statistically centered on the points of a distorted hexagonal lattice. The variations in the mesopore centers and radii add up and result in pore wall corrugation with amplitude of 1.6 nm. The correlation length of the corrugation along the pore axis was found to be 4-5 nm. The amplitude of the corrugation compared well with the 1.9 nm thick microporous corona obtained from X-ray diffraction (XRD). In general, the present approach provides a detailed microscopic 3D model of nanostructured materials that complements macroscopic measurements such as physisorption and XRD.