Today, the manipulation and integration of objects with nanometric dimensions is essential for a great number of applications. In biology and medicine, the study of structural dynamics in individual molecules or other key cellular processes is often limited by the low throughput of current methods. Here, we will demonstrate how nanopatterning could yield improvements relative to current practice for single molecule assays, by increasing the density and organization as opposed to random deposition. In fact, we have explored the combination of soft-lithography with a directed capillary assembly technique . As a proof of concept, we have demonstrated that by using this methodology we are able to control the assembly of different objects ranging from cells, to molecules and nanoparticles, at accurate positions and at high yield while preserving their functionality [2-4]. As an extension of these results, we will show that we are capable of multiplexing sequences in a field of view and capable of including imaging-enhancing structures colocated with DNA tethers. This will lead to the construction of a robust experimental platform allowing massively parallel data collection at the single molecular level in real time and under various conditions.