The ability to selectively tune the optical properties of two-dimensional (2D) materials at specific sites is of great interest for the development of optoelectronic and photonic devices. We report site-specific electron-beam (e-beam) induced deposition for creating patterned carbon nanostructures on atomically thin 2D materials such as WS₂ and MoS₂. Various patterns ranging from microns to nanometres in size have been produced and controlled by adjusting e-beam parameters such as accelerating voltage, spot size, magnification, and irradiation time. The ultimate pattern dimensions of ∼52 nm in width and ∼2.58 nm in height is achieved. The patterned areas exhibit a quenching of fluorescence intensity of about three times, making it simple to identify the created structure from the 2D materials. Moreover, Kelvin probe force microscopy measurements indicated that the surface potential of the patterned sites is roughly 95.6 mV different from that of non-patterned WS₂. Finally, we have demonstrated optical encryption by selectively integrating carbon structures to modulate the optical emission of WS₂.