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Controlled chemical transformation of nanostructures is a promising technique to obtain precisely designed novel materials which are difficult to synthesize otherwise. We report high-temperature vapor phase anion exchange reactions to chemically transform II-VI semiconductor nanostructures (100-300 nm length scale) while retaining the single crystallinity, crystal structure, morphology and even defect distribution of the parent material via atomic templating. The concept of atomic templating is employed to obtain kinetically controlled, thermodynamically metastable structural phases such as zincblende CdSe and CdS from zincblende CdTe upon complete chemical replacement of Te with Se or S. The underlying transformation mechanisms are explained through first-principles density functional theory calculations. Atomic templating is a unique path to independently tune materials phase and composition at the nanoscale allowing synthesis of novel materials.