Close-packed pyramidal assemblies of 100 nm latex nanoparticles were made by convective/capillary deposition on hydrophilic patterns created by oxidation lithography using atomic force microscopy (AFM). We demonstrated that the substrate temperature during convective/capillary assembly is a key experimental parameter in finely tuning the geometry of these pyramids and thus the total number of nanoparticles forming each 3D assembly. The volume and shape of these nanoparticle assemblies are discussed and compared to simulations.