Control over the atomic structure of nanoscale materials allows for tailoring of their electronic and physical properties to enhance or alter their applications. The elemental and structural makeup of the nanomaterials dictates which methods of atomic control can be utilized to tailor their atomic structure. In this dissertation, we focus on nanomaterials comprised of low-dimensional building blocks, such as graphene, hexagonal boron nitride (h-BN), and transition metal chalcogenides (TMC), all members of the class of van der Waals (vdW) structures. We will leverage the 2-dimensional (2-D) and 1-D vdW nature of these nanomaterial systems to tailor their atomic and electronic structure through doping, conversion, or confinement.Part I will open our discussion on targeted material growth, utilizing synthetic chemistry techniques to reconfigure a nanomaterial’s atomic and electronic structure through doping and conversion. The work presented in Chapters 1-5 focuses on the concept of dimensionality and how it relates to material structure, property, and applications. Chapter 3 analyzes synthetic chemistry techniques used to alter the structure of graphene sheets and assemble those sheets into graphene-based macrostructures, such as doped-aerogels, for more meaningful applications. Chapter 4 examines methods to utilize the robust lattice of graphene as scaffolding for the conversion of other porous, macroscopic systems built from other 2-D materials, such as h-BN nanofoams. Chapter 5 explores the conversion method to access different compositions of porous structures beyond that of a layered material, breaking into the porous ceramics field. Part II examines other vdW nanoscale materials from the TMC, such as the transition metal dichalcogenides (TMD) and trichalcogenides (TMT). However, techniques discussed in Part I are not easily applied to the TMD and TMT to tailor their atomic and electronic structure. Therefore, we pursue other means of atomic tailoring, specifically constrained material growth, where the atomic and electronic structure of materials can be reconfigured through drastic physical confinement of the crystals grown. Chapters 8-14 studies how constraining the dimensions of these 2-D and 1-D vdW materials down to “atomic thinness” results in size quantization with profound consequences. Confinement through nanotube encapsulation of the TMD and TMT nanomaterials has resulted in several emergent phenomena ranging from structural distortions (Chapters 8 and 9) to newly stabilized crystalline structures (Chapters 10, 11, and 13) to periodic superstructures (Chapters 12 and 14).