The performance of graphene devices is often limited by defects and impurities induced during device fabrication. Polymer residue left on the surface of graphene after photoresist processing can increase electron scattering and hinder electron transport. Furthermore, exposing graphene to plasma-based processing such as sputtering of metallization layers can increase the defect density in graphene and alter the device performance. Therefore, the preservation of the high-quality surface of graphene during thin-film deposition and device manufacturing is essential for many electronic applications. Here, we show that the use of self-assembled monolayers (SAMs) of hexamethyldisilazane (HMDS) as a buffer layer during the device fabrication of graphene can significantly reduce damage, improve the quality of graphene, and enhance device performance. The role of HMDS has been systematically investigated using surface analysis techniques and electrical measurements. The benefits of HMDS treatment include a significant reduction in defect density compared with as-treated graphene and more than a 2-fold reduction of contact resistance. This surface treatment is simple and offers a practical route for improving graphene device interfaces, which is important for the integration of graphene into functional devices such as electronics and sensor devices.