An array of Nano-protrusions (NPs) was fabricated on silicon surfaces in air and a low pressure environment using pulsed laser irradiation. The uniformly sized NPs were linearly aligned at a low laser energy density, which is typically a few kilojoules per square meter. The linear array of NPs appeared perpendicular to the laser polarization vector E, and the interval of the NPs lines was almost equal to the wavelength of the incident laser. The primary NPs grew epitaxially and were covered with an oxide film layer, which was determined by means of a structural and elemental analysis using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy-dispersive X-ray spectroscopy (EDS). We propose a nano-patterning fabrication method using the laser-induced NPs alignment based on a microscopic structural analysis.