Composite nanomaterials are attractive for a diverse range of applications in catalysis, plasmonics, sensing, imaging, and biology. In such composite nanomaterials, it is desired, yet still challenging to create a controlled alignment between components with lattices in disparate scales. To address this challenge, we report a new concept of colloidal synthesis, in which self-assembled molecular layers control the alignment between materials during the synthesis. To illustrate this concept, self-assembled cetyltrimethylammonium bromide (CTAB) molecules are used to control interfaces in a core-shell nanocomposite with a well-defined metal nanocrystal core and a metal-organic-framework (MOF) shell, which differ in structural dimensions by orders of magnitude. We show that single metal nanocrystals are captured individually in single-crystalline MOFs, and an alignment between the {100} planes of the metal and {110} planes of the MOFs is observed. By utilizing the same concept, a layer of mesostructured silica is formed over MOF crystals. These multilayered core-shell structures demonstrate a controlled alignment across a wide range of materials, from the metal nanocrystals, extending to nanoporous MOFs and mesostructured silica.