A reliable strategy is presented to combine the preparation of functional building blocks based on polymer beads decorated with luminescent nanocrystals (NCs) and their precise positioning onto suitable patterns by capillary assembly technique. In particular, a layer-by-layer (LbL) polyelectrolyte (PE) deposition procedure has been implemented to provide uniform NC coverage on PS beads, thus conveying the optical properties of luminescent nanocrystals to highly processable PS beads. The latter have then been integrated into patterned stamps by means of template-driven capillary assembly. Their selective positioning has been directed by means of pattern geometry. The use of luminescent (CdSe)ZnS NCs offers a direct optical probe to evaluate the efficiency of the positioning procedure on the substrate, enabling the extension of the method to a wide range of materials, i.e., NCs with different compositions and specific geometry-dependent properties. Moreover, the precise control over the pattern geometry and the micrometer accuracy in positioning achieved by capillary assembly make such functional patterned structures excellent candidates for integration into devices exploiting specific size-dependent NC properties.