Materials at the nanoscale have revolutionized the world around us by enabling the discovery of novel size dependent properties and experimental verification of untested theoretical concepts. However, most nanomaterials today are phases of matter that are well known and have been studied extensively at the bulk scale. For example, II-VI semiconductors, which are widely studied today at the nanoscale, were employed in photovoltaic applications at the microscale for nearly half a century. The question that arises is whether material processing at the nanoscale can allow us to go beyond the limitations of conventional synthesis techniques? We believe that the next pathbreaking step in nanotechnology is to synthesize novel phases of materials which are metastable by thermodynamic considerations and hence challenging to achieve through established one-step synthesis processes. At the core of such an approach is the desire to gain in-depth scientific understanding of the chemical and morphological transformation mechanisms that enable the engineering of novel nanomaterials with exotic physical properties. Our research revolved around synthesizing novel nanomaterials from preexisting nanostructures via chemical and morphological transformation in a chemical vapor deposition system while preserving the morphology and atomic arrangement of the parent material through, what we like to call, “atomic templating”. We explored chemical transformation in II-VI semiconducting nanostructures via anion exchange to synthesize metastable phases of materials such as zincblende CdS and CdSe while retaining the crystal structure and twin boundaries of the parent zincblende CdTe. We later extended the concept of atomic templating to explore chemical substitution in II-VI semiconductors with elements from dissimilar groups of the periodic table such as IV A and V A that possess different bonding characteristics with chalcogenides as compared to elements of group II B. We also studied chemical substitution in a covalently bonded compound, GeTe. Finally, morphological transformation of CdS nanobelts into periodically branched nanostructures was studied through environmental TEM. The resulting nanostructures were thoroughly characterized via electron microscopy, photoluminescence and Raman spectroscopy. Through first principles calculations via density functional theory, experimental observations were explained and novel physical properties targeted at specific applications were predicted.