Self-assembly (SA) is a bio-inspired key coordination mechanism for swarms of intelligent agents as well as a pervasive bottom-up methodology for the fabrication of heterogeneous micro- and nanosystems. Analytical studies of SA at small scales are therefore highly relevant for many technological applications. In this paper we present an innovative design and fabrication process for three-dimensional polymeric microtiles conceived as passive vehicles to investigate the dynamics of fluidic SA at sub-millimeter scale. The microtiles are fabricated out of the superposition of two structural SU-8 layers featuring chiral copies of the same centro-symmetric pattern. They can coordinate laterally in water independently of their vertical orientation to form close-packed square lattice clusters. The microtiles embed a central marker enabling the real-time optical tracking and automated closed-loop control of their fluidic SA. The fabrication process makes use of a thick sacrificial copper layer and allows the wafer-level batch production of tens of thousands of microtiles, in line with the massively parallel nature of SA.