Precise modulation of electrical and optical properties of 2D transition metal dichalcogenides (TMDs) is required for their application to high-performance devices. Although conventional plasma-based doping methods have provided excellent controllability and reproducibility for bulk or relatively thick TMDs, the application of plasma doping for ultrathin few-layer TMDs has been hindered by serious degradation of their properties. Herein, a reliable and universal doping route is reported for few-layer TMDs by employing surface-shielding nanostructures during a plasma-doping process. It is shown that the surface-protection oxidized polydimethylsiloxane nanostructures obtained from the sub-20 nm self-assembly of Si-containing block copolymers can preserve the integrity of 2D TMDs and maintain high mobility while affording extensive control over the doping level. For example, the self-assembled nanostructures form periodically arranged plasma-blocking and plasma-accepting nanoscale regions for realizing modulated plasma doping on few-layer MoS2, controlling the n-doping level of few-layer MoS2 from 1.9 x 10(11) cm(-2) to 8.1 x 10(11) cm(-2) via the local generation of extra sulfur vacancies without compromising the carrier mobility.