The chemical potential difference between homopolymer fractions in block copolymers can be readily used to selectively design, and cooperatively assemble, inorganic species into highly ordered three-dimensional (3d) periodic composite arrays of separated mesoscale regions. The actual details and symmetry of these regions and their long-range order can only be determined by 3d imaging and analysis with high-resolution electron microscopy (HREM). Of particular interest is the differentiation between configurations with very similar organization energies, such as the cubic and hexagonal (SBA-2) closed-packed structures. Mesoporous silica SBA-12 and functionalized SBA-12 (SH-SBA-12) have been synthesized from the 3-mercaptopropyl group by using nonionic surfactant C18H37(CH2CH2O)(10) (C18EO10, Brij 76) under acidic hydrothermal condition. Relatively large single-phase domains were obtained in SH-SBA-12. The 3d structural solution of SH-SBA-12 was obtained by Fourier analyses of HREM images. The structure is composed of spherical cavities, which are arranged in a cubic close-packed structure, in which each cavity is connected to the twelve nearest-neighbor cavities through openings parallel to the (110) directions. HREM images of SBA-12 taken over large sample regions show that SBA-12 is a mixture of mostly the cubic close-packed phase, which consist of beautifully crystalline narrow bands with the same 3d structure in twin relation to each other and a relatively small amount of the 3d hexagonal close packed phase.