In this work a genuine combination of a bottom-up approach, which is based on synthesis and functionalization of emitting nanocrystals (NCs), with a top-down strategy, which relies on a flexible and versatile cold plasma process, is shown. Luminescent semiconducting colloidal NCs consisting of a CdSe core coated with a ZnS shell (CdSe@ZnS) are directly assembled onto micro-patterned substrates previously functionalized by means of glow discharges performed through physical masks. The NC assembly is driven by electrostatic interactions that led to their successful organization into spatially resolved domains. Two distinct protocols are tested, the former using a plasma deposition process combined with an electrostatic layer-by-layer procedure, the latter based on a two-step plasma deposition/treatment process. The procedures are thoroughly monitored with fluorescence microscopy, atomic force microscopy, x-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, transmission electron microscopy and scanning electron microscopy. The two-step plasma protocol is demonstrated to be more efficient in directing a uniform and specific assembly of luminescent NCs with respect to the hybrid procedure. The presented 'mix and match' approach offers great potential for integrating NCs, with their unique size-dependent properties, into microstructures, providing a universal platform for the fabrication of sensors, biochips, displays and switches.