In this paper, we show that it is possible to direct the adhesion of polyelectrolyte microcapsules to patterned substrates. The patterned substrate contains regions of like and oppositely charged polyelectrolyte coatings: Adhesion of microcapsules is blocked by regions of the substrate containing like charges, while we find strong adhesion on oppositely charged regions. The approach is completely based on self-assembly and can be performed under ambient laboratory conditions. We demonstrate that it is thus possible to isolate individual microcapsules, with enclosed volumes on the order of femtoliters, and create arrays. This strategy could find applications in the field of combinatorial chemistry or sensing techniques where the capsules can serve as reaction volumes or containers for sensing agents, respectively.