Chemical vapor deposition (CVD) is one of the most versatile techniques for the controlled synthesis of functional nanomaterials. When multiple precursors are induced, the CVD process often gives rise to the growth of doped or alloy compounds. In this work, we demonstrate the self-assembly of a variety of 'phase-separated’ functional nanostructures from a single CVD in the presence of various precursors. In specific, with silicon substrate and powder of Mn and SnTe as precursors, we achieved self-organized nanostructures including Si/SiO_x core-shell nanowire heterostructures both with and without embedded manganese silicide particles, Mn₁₁Si₁₉ nanowires, and SnTe nanoplates. The Si/SiO_x core-shell nanowires embedded with manganese silicide particles were grown along the <111> direction of the crystalline Si via an Au-catalyzed vapor-liquid-solid process, in which the Si and Mn vapors were supplied from the heated silicon substrates and Mn powder, respectively. In contrast, direct vapor-solid deposition led to particle-free <110>-oriented Si/SiO_x core-shell nanowires and <100>-oriented Mn₁₁Si₁₉ nanowires, a promising thermoelectric material. No Sn or Te impurities were detected in these nanostructures down to the experimental limit. Topological crystalline insulator SnTe nanoplates with dominant {100} and {111} facets were found to be free of Mn (and Si) impurities, although nanoparticles and nanowires containing Mn were found in the vicinity of the nanoplates. While multiple-channel transport was observed in the SnTe nanoplates, it may not be related to the topological surface states due to surface oxidation. Finally, we carried out thermodynamic analysis and density functional theory calculations to understand the 'phase-separation’ phenomenon and further discuss general approaches to grow phase-pure samples when the precursors contain residual impurities.