Direct knowledge of crystal defects and their perturbation of magnetic flux lines is essential to understanding pinning and to devising approaches that enhance critical currents in superconductors with high critical temperatures (T-c). Atomic force microscopy was used to simultaneously characterize crystal defects and the magnetic flux-line lattice in single crystals of Bi2Sr2CaCu2O8. Images show that surface defects, which are present on all real samples, pin the flux-line lattice. Above a critical height, the pinning interaction is sufficiently strong to form grain boundaries in the bulk flux-line lattice. These results elucidate the structure of the defects that pin flux lines and demonstrate that surface pinning, through the formation of grain boundaries, can determine the bulk flux-line lattice structure in high-T-c materials. The implications of these results to the bulk flux-line lattice structure observed in previous experiments and to enhancing critical currents are discussed.