The substrate wetting of an amorphous, low-glass-transition-temperature spherical poly(isoprene-block-ferrocenylsilane) (PI-b-PFS) block copolymer and the alignment of the microdomains in grooves of various geometry are studied. Compositional analysis by time-of-flight secondary ion mass spectrometry depth profiling (TOF-SIMS) indicates the presence of both PI and PFS directly at the film–substrate interface on silicon and silica substrates. The TOF-SIMS depth-profiling study indicates a transition in the packing of the domains between the two-dimensional (2D) monolayer and 3D, thicker layers. In a monolayer of domains, a hexagonal packing is adopted. In films of two or three layers, the hexagonal packing reorganizes towards a body-centered cubic (bcc) packing by the extension of the copolymer chains in the direction normal to the substrate, as indicated by an increase in spacing between PFS layers and an increase in domain size. For thicker layers, a bcc morphology with the (110) plane parallel to the substrate is found to extend from the free surface downwards. Films of one monolayer of domains of the copolymer exhibit long-range lateral ordering on the micrometer scale on flat substrates without high-temperature annealing. On topographically patterned silicon substrates the position of the domains of the minority PFS phase directly near the side walls is fixed by the neutral wetting condition. Successful positioning of the block-copolymer spheres in linear and hexagonal grooves is achieved in grooves up to 1.3 μm wide, whereby the hexagonal grooves demonstrate complete 2D alignment. In circular pits, this graphoepitaxial effect is absent.