The assembly of colloidal crystals can be assisted by the application of external fields such as flow or sedimentation. These processes to form colloidal crystals are of technological interest because of applications in, for example, photonic band gap materials and sensors. However, for such applications, assembly ideally should yield macroscopic crystals with low defect density. Although colloidal crystallization during, for example, shear deformation has been demonstrated to grow large crystallites, the way in which the flow mediates the assembly, defect density and crystal structure is not fully understood. Here we use confocal laser scanning microscopy (CLSM) to directly visualize the real-space structure of ordered arrays of colloidal spheres formed by shear flow and sedimentation. The colloids are micron-size, fluorescent monodisperse poly(methyl methacrylate) spheres dispersed in nearly refractive index matched solvents. Local structure is quantified by means of bond orientational parameters and stacking fault identification. We evaluate the effect of shear flow (strain rate and amplitude) on local ordering. We compare stacking fault structures produced by means of shear flow and by sedimentation. We consider the effect of pair potential interactions on field-assisted assembly.