This study presents a new, simple, and low-cost technique to fabricate a nanocluster silicon (NCSi) surface on planar silicon using a micro-scale direct current (DC) discharge under ambient conditions. The method requires no masks, chemicals, vacuum environment, or laser, but only a high-voltage supply. The NCSi surfaces, characterized by scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy, consist of oxidized silicon nanoclusters 50–200 nm in diameter, likely formed by melting due to high temperatures in the discharge. The minimum size of the NCSi spot is determined by the size of the discharge tip (∼90 µm). Arbitrary NCSi areas can be produced on a silicon wafer by moving the discharge needle on the surface with the help of a computer-controlled xyz stage. NCSi surfaces can also be formed on three-dimensional (3D) surfaces, as demonstrated with silicon micropillars. NCSi surfaces can be used, for example, in various analytical applications. In this study, we demonstrate their use as sample plates in the analysis of drugs and peptides with desorption/ionization on silicon-mass spectrometry (DIOS-MS).