In recent years, two-dimensional Transition Metal Dichalcogenide (TMDC) materials such as MoS2 have drawn considerable interest due to their intriguing electrical, optical, sensing, and catalytic properties [Castellanos-Gomez et al. 2012]. While Graphene-based devices have shown high carrier mobility up to ~ 105 cm2/Vs [Bolotin et al. 2008] and cut-off frequency higher than ~ 100 GHz [Liao et al., 2010], the inherent zero – band gap electronic structure of graphene results in high OFF state current. On the other hand, monolayer MoS2 is a semiconductor with a direct band gap of ~1.9eV [Mak et al. 2010]. MoS2 transistors are a promising alternative for the semiconductor industry due to their large ON/OFF current ratio (> 10e10) [Yoon et al., 2011], immunity to short channel effects, and abrupt switching. However, realization of practical mono/few layer MoS2 devices is limited by the free charge density in intrinsic MoS2 (10e10/cm2) [Rastogi et al. 2014]. The objective of this work is to utilize He-ion beam patterning to write pattern of vacancies (< 10 nm) onto CVD synthesized 2D MoS2. The vacancies thus generated are then doped via molecular doping technique to improve upon the intrinsic free carrier concentration in 2D MoS2. Briefly, the method is as follows. (a) First, highly crystalline 2D MoS2 are synthesized on SiO2/Si substrate using MoO3 and S powder as the precursors in a CVD furnace. (b) Next, He-ion beam patterning is used to generate vacancies in only the very top S layer. The shorter de Broglie wavelength of He-ions allows for milling at higher resolution than other charged particle microscopes. (c) Next, solution-based molecular doping method is used to realize non-degenerate n-type doping in 2D MoS2. This is accomplished by soaking the patterned 2D layers in 1, 2-dichloroethane (DCE) solution at room temperature for about 12 hours. As a result, the patterned vacancies are occupied by Cl atoms which donate the extra electrons to the MoS2 system. The electronic properties are tuned by varying the MoS2 layer thickness and solution concentration. Post-doping, the electrostatic properties are measured by using PL measurements and different modes of AFM, including Kelvin force microscopy (KFM) and Scanning microwave microscopy (SMM). An important contribution of this work is the presentation of optimized He-ion beam conditions, including the accelerating voltage and the effects of defect generation on the sub-surface layers. He-ion beam based defect generation creates a shallow penetration depth, which makes them more suitable for single S vacancies. Finally, the changes in the surface potential and a quantitative analysis of the dopant density were measured suing KFM and SMM respectively, indicating that doping is in the non-degenerate regime.