• Abstract Two-dimensional (2D) materials, such as graphene, transition metal dichalcogenides (TMDs) and hexagonal boron nitride, exhibit intriguing properties that are sensitive to their atomic-scale structures and can be further enriched through van der Waals (vdW) integration. • However, the precise synthesis and clean integration of 2D materials remain challenging. • Here, using graphene or hexagonal boron nitride as a vdW capping layer, we create a nano-confined environment that directs the growth kinetics of 2D TMDs (such as NbSe2 and MoS2), enabling precise formation of TMD monolayers with tailored morphologies, from isolated monolayer domains to large-scale continuous films and intrinsically patterned rings. • Moreover, Janus S-Mo-Se monolayers are synthesized with atomic precision via vdW-protected bottom-plane chalcogen substitution. • Importantly, our approach simultaneously produces ultraclean vdW interfaces. • This in situ encapsulation reliably preserves air-sensitive materials, as evidenced by the enhanced superconductivity of nano-confined NbSe2 monolayers.
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