We present an ultra-high vacuum scanning tunneling microscopy (STM) study of structural defects in molybdenum disulfide thin films grown on silicon substrates by chemical vapor deposition. A distinctive type of grain boundary periodically arranged inside an isolated triangular domain, along with other inter-domain grain boundaries of various types, is observed. These periodic defects, about 50 nm apart and a few nanometers in width, remain hidden in optical or low-resolution microscopy studies. We report a complex growth mechanism that produces 2D nucleation and spiral growth features that can explain the topography in our films.The many incredible properties of graphene including high carrier mobility (200,000 cm 2 V −1 s −1 ) 1 have made it a very special material both from fundamental science and an engineering point of view. However, the lack of a band-gap in graphene causes high leakage current which makes it unsuitable for many optoelectronic purposes and logic-based devices and circuits. In contrast, transition metal dichalcogenides (TMDs) with the general chemical formula MX2 (M = Mo, W; X = S, Se, Te) provide a large family of two-dimensional (2D) crystals that vary greatly in physical and chemical properties 2 , ranging from metallic to semiconducting to insulators. Of all the TMDs, molybdenum sulfide (MoS2), with its indirect-to-direct band gap transition as a function of layer thickness, has been of particular interest for digital and optoelectronic applications. MoS2 has already been used to fabricate functional electronic circuit elements 3-6 , as well as used for optoelectronics 7-9 , valleytronics, spintronics 10, 11 and coupled electro-mechanics 12 .Most of the MoS2 material characterization and device demonstrations so far have been on exfoliated samples which suffer from low yield, and cannot be scaled up for practical applications. In order to address these problems, significant work has been done to introduce different growth techniques. Processes including liquid exfoliation 13 and direct sulfurization of molybdenum thin films 14 have been achieved to synthesize large MoS2 monolayers. However, the overall simplicity and the high quality of films obtained using the sulfurization of MoO3 has made it one of the most widely used methods of synthesizing large area monolayer MoS2 15-17 .Just like different synthesis techniques, various analytical techniques have been introduced. In addition to the commonly used techniques like scanning electron microscopy (SEM) and atomic force microscopy (AFM), techniques like Raman and photoluminescence (PL) spectroscopy have become common to ascertain the number of layers of these 2D materials. However, because of the resolution limit, these techniques only reveal a partial picture. SEM and AFM together show us the topographical and structural information. The spectroscopic techniques ascertain the energy levels to a certain degree. Recent techniques like microwave impedance microscopy (MIM) 18 have been used to map the dielectric constant of these films. Howev...