Fluid-mediated self-assembly is one of the most promising routes for assembling and packaging smart microsystems in a scalable and cost-efficient way. In this work the pairwise fluidic self-assembly of 100 μm-sized SU-8 cylinders is studied with respect to two driving mechanisms: capillary forces at the liquid–air interface and the hydrophobic effect while fully immersed in liquid. The pairwise self-assembly is controlled by shape recognition and selective surface functionalization. Surface energy contrast is introduced through oxygen plasma treatment and local deposition of a hydrophobic self-assembled monolayer, respectively leading to face-selective hydrophilic and hydrophobic behavior. When in bulk liquid, after less than a day face-wise self-assembly of more than 650 components is achieved with a yield of up to 97% and with less than 1% of the cylinders assembled incorrectly. This technique is subsequently adopted for self-assembling half-capsules into closed micro-capsules, thereby entrapping a liquid during their self-assembly. The release of the liquid can subsequently be triggered in another medium, as intended for applications involving e.g. chemical reactors, environmental engineering and drug release.