Two-dimensional (2D) transition metal dichalcogenides are pivotal for next-generation photonic devices due to their exceptional optical properties and strong light-matter interactions. However, their atomic thinness renders them susceptible to damage during nanoscale fabrication. Focused ion beam technology, while offering precise defect engineering for tailoring optoelectronic properties, often induces collateral damage far beyond the target region, compromising device performance. This study addresses the critical challenge of preserving the intrinsic optical characteristics of 2D TMDCs during FIB patterning. We demonstrate that conventional dielectric encapsulation fails to protect 2D TMDCs from gallium ion-induced damage, leading to persistent defects and quenched optical responses in patterned microstructures. In contrast, polymeric encapsulation with PMMA (polymethyl methacrylate) effectively mitigates damage by acting as a sacrificial layer that absorbs ion impact, thereby preserving the optical properties of the underlying TMDC. Furthermore, we leverage XeF2-assisted Ga ion beam direct patterning, which significantly reduces collateral damage, minimizes Ga ion implantation, and enables precise anisotropic material removal, yielding ultra-smooth sidewalls critical for high-quality photonic resonators. This combined approach of PMMA encapsulation and XeF2-assisted FIB patterning offers a robust, cost-effective, and scalable single-step fabrication route for integrating 2D TMDCs into high-performance photonic devices, thereby maintaining their intrinsic optical functionality essential for advancing quantum technologies and compact optical circuits.