Novel two dimensional nanoscale materials like graphene and metal dichalcogenides (MX2) have attracted the attention of the scientific community, due to their rich physics and wide range of potential applications. It has been shown that novel graphene based transparent conductors and radiofrequency transistors are competitive with the existing technologies. Graphene’s properties are influenced sensitively by adsorbates and substrates. As such not surprisingly, physical properties of graphene are found to have a large variability, which cannot be controlled at the synthesis level, reducing the utility of graphene. As a part of my doctorate dissertation, I have developed atomic hydrogen as a novel technique to count the scatterers responsible for limiting the carrier mobility of graphene field effect transistors on silicon oxide (SiO2) and identified that charged impurities to be the most dominant scatterer. This result enables systematic reduction of the detrimental variability in device performance of graphene. Such sensitivity to substrates also gives an opportunity for engineering device properties of graphene using substrate interaction and atomic scale vacancies. Stacking graphene on hexagonal boron-nitride (h-BN) gives rise to nanoscale periodic potential, which influences its electronic graphene. Using state-of-the-art atomic-resolution scanning probe microscope, I correlated the observed transport properties to the substrate induced extrinsic potentials. Finally in efforts to exploit graphene’s sensitivity to discover new sensor technologies, I have explored noncovalent functionalization of graphene using peptides. Molybdenum disulfide (MoS2) exhibits thickness dependent bandgap. Transistors fabricated from single layer MoS2 have shown a high on/off ratio. It is expected that ad-atom engineering can be used to induce on demand a metal-semiconductor transition in MoS2. In this direction, I have iii explored controlled/reversible fluorination and hydrogenation of monolayer MoS2 to potentially derive a full range of integrated circuit technology. The in-depth characterization of the samples is carried out by Raman/photoluminescence spectroscopy and scanning tunneling microscopy