A detailed study of the three-dimensional (3-D) confinement of polystyrene-block-poly(ferrocenylethylmethylsilane) (PS-b-PFS) diblock copolymers in silica colloidal crystals and inverse silica colloidal crystals is reported. Inversion of the silica colloidal crystal lattice with PS-b-PFS is confirmed by scanning electron microscopy and optical spectroscopy. Additionally, the modification of the silica surfaces in the inverse colloidal crystals using hydroxy-terminated PS and PFS is established. The 3-D confined morphologies of a lamella-forming and a cylinder-forming PS-b-PFS diblock copolymer are subsequently investigated. The manipulation of the 3-D confined morphology of cylinder-forming PS-b-PFS is demonstrated by deliberate alteration of its wetting interaction with the surface-modified colloidal crystal templates. Unprecedented 3-dimensional block copolymer morphology transitions are elucidated.