Using nanoimprint lithography, arrays of highly ordered patterns of polyelectrolyte multilayer microcapsules consisting of alternating layers of poly(allylamine hydrochloride) and poly(sodium 4-styrene sulfonate) have been achieved. Anchoring the capsules on a pre-patterned substrate facilitates the utilization of their various capabilities in lab-on-a chip devices. In this paper we have demonstrated a very effective method to entrap soft capsules into surface cavities. Supported microcapsules were applied as the depots for loading and storage of macromolecular cargo (glucose oxidase and peroxidase) and as preserved microvessels for the cascade of enzymatic reactions. The loading of capsules was achieved under a pre-determined pH environment. This development is potentially useful for the realization of novel multianalytical systems for catalytic, bio-affinity and pH detection with protected sensing molecules.