Functional materials that are active at nanometer scales and adaptive to environment have been highly desirable for a huge array of novel applications ranging from photonics, sensing, fuel cells, smart materials to drug delivery and miniature robots. These bio-inspired features imply that the underlying structure of this type of materials should possess a well-defined ordering as well as the ability to reconfigure in response to a given external stimulus such as temperature, electric field, pH or light. In this thesis, we employ computer simulation as a design tool, demonstrating that various ordered and reconfigurable structures can be obtained from the self- and directed-assembly of soft matter nano-building blocks such as nanoparticles, polymer-tethered nanoparticles and colloidal particles. We show that, besides thermodynamic parameters, the self-assembly of these building blocks is governed by nanoparticle geometry, the number and attachment location of tethers, solvent selectivity, balance between attractive and repulsive forces, nanoparticle size polydispersity, and field strength. We demonstrate that higher-order nanostructures, i.e. those for which the correlation length is much greater than the length scale of individual assembling building blocks, can be hierarchically assembled. For instance, bilayer sheets formed by laterally tethered rods fold into spiral scrolls and helical structures, which are able to adopt different morphologies depending on the environmental condition. We find that a square grid structure formed by laterally tethered nanorods can be transformed into a bilayer sheet structure, and vice versa, upon shortening, or lengthening, the rod segments, respectively. From these inspiring results, we propose a general scheme by which shape-shifting particles are employed to induce the reconfiguration of pre-assembled structures. Finally, we investigate the role of an external field in assisting the formation of assembled structures that would not be accessible from self-assembly. As an example, we show the assembly of magnetic Janus particles with a highly ordered alignment and a tunable gradient density, which are likely to be applicable to photonic band gap materials. Our results and proposed methods serve not only as proofs of concept for designing functional nanostructured materials via "bottom-up" approaches, but also to inspire further theoretical and experimental investigations.