Pillar-like structures of nanodiamonds on a silicon substrate are self-assembled for the first time by a pulsed spray technique. This technique allows us to deposit nanodiamond layers by using high quality nanocrystals of 250 nm dispersed in 1,2-dichloroethane (DCE) solvent. The analysis of 2D/3D confocal and atomic force microscopy images evidences the presence of self-assembled pillar-like structures distributed in an irregular way. The proposed method is simple, easy and cheap, and does not require complex growth processes or structured materials, ideal for upscaling toward industrial biochip implementation and photonic applications. The suggested formation mechanisms of self-assembly are based on the so-called coffee stain effect, i.e., on the time evolution of DCE evaporation.