In living things self-assembly is a widely used and robust manufacturing tool: DNA, RNA and proteins spontaneously form three dimensional structures, and supramolecular structures emerge from protein aggregates with staggering degrees of ordering and specificity. On the other hand, most colloidal systems do not, in general, assemble robustly into ordered structures. Perhaps the primary difficulty with using colloidal self-assembly as a nanofabrication method is the large number of mechanically stable conformations available to a system of N identical, spherical colloidal particles. Using experimental model systems of small numbers of confined colloidal particles, we probe the number of configurations observed under equilibrium and non-equilibrium (quenched)conditions. To do this we use an experimental technique known as digital holographic microscopy, which allows us to probe the dynamics and structure of these systems in three dimensions with millisecond time resolution and nanometer-scale spatial precision. The results from these small model systems can be compared directly to simulation and theory. Based on these results we have developed some general strategies for using biomolecular functionalization to enforce robust self-assembly in colloidal system.