We have studied the assembly of 3-D colloidal crystals from binary mixtures of colloidal microspheres and highly charged nanoparticles on flat and epitaxially patterned substrates created by focused ion beam milling. The microspheres were settled onto these substrates from dilute binary mixtures. Laser scanning confocal microscopy was used to directly observe microsphere structural evolution during sedimentation, nanoparticle gelation, and subsequent drying. After microsphere settling, the nanoparticle solution surrounding the colloidal crystal was gelled in situ by introducing ammonia vapor, which increased the pH and enabled drying with minimal microsphere rearrangement. By infilling the dried colloidal crystals with an index-matched fluorescent dye solution, we generated full 3-D reconstructions of their structure including defects as a function of initial suspension composition and pitch of the patterned features. Through proper control over these important parameters, 3-D colloidal crystals were created with low defect densities suitable for use as templates for photonic crystals and photonic band gap materials.