Nanoparticle (NP) self-assembly from suspension evaporation has been a topic of interest in recent times to fabricate a solid-state structure with diverse functions. We present a simple and facile evaporation-induced strategy for the formation of NP arrays on a flat substrate utilizing a template-directed sandwich system. The lithographic features assist the assembly of the typical nanoparticles (NPs), including SiO2, QDs@PS FMs, and QDs, on the top into circle, stripe, triangle, or square geometries with a fixed width of 2 μm. Additionally, an anionic surfactant, sodium dodecyl sulfonate (SDS), is incorporated into a negatively charged, hydrophilic SiO2 dispersion to govern the aggregation and self-assembly of NPs, fine tuning the morphologies of the residual structures on the substrate. SDS is attributed to modify the nature of SiO2 NPs to be hydrophobic, increase the hydrophobic attraction, dominating particle-particle and particle-interface interactions, and strengthen the particle-particle repulsive electrostatic force that results in the reduction of SiO2 NPs trapped in the separated colloidal suspension drop. Thus, using the SDS surfactant with the concentration ranging from 0 to 1 wt %, the obtained well-ordered SiO2 NP pattern packing on the substrate varies from six layers to one layer.