Nanocomposite materials exhibit properties that highly depend on the organization of nanoparticles. Currently, the ability to control the arrangement of nanoscale building blocks has become one of the most important issues in the field. In this thesis, I present a unique way to control the arrangement of nanoparticles in polymer matrixes by the self-assembly of amphiphilic block copolymers and nanoparticles. Unique capsule-like assemblies of nanoparticles were formed by controlling the interaction between nanoparticles and a prototypical block copolymer, PAA-b-PS. This layered structure is composed of a polymer core, a polymer shell and nanoparticles encapsulated between the polymer core and the shell. This unique assembly structure is induced by slightly unfavorable interactions between the polystyrene and nanoparticles. The strong segregation theory calculations showed that the reduced stretching energy of polymers by the incorporation of nanoparticle layer also contributed to the formation of the layered structure. Many parameters such as nanoparticle volume fraction, nanoparticle size, polymer length and nanoparticle capping agents affect the arrangement of nanoparticles as well as the overall assembly structure of the composite system. In particular, it was found that the radial location of nanoparticle in the core shell assembly can be effectively tuned by controlling the volume fraction of nanoparticles. This work demonstrated for the first time that it is possible to form ordered arrays of nanoparticles with controllable assembly structure through the self-assembly of nanoparticles and amphiphilic polymers. Polymer nanostructures were also used as templates to synthesize a new type of metal nanostructures called spiky gold nanoshells. Block copolymer assemblies of different morphologies were used to template non-spherical nanoshells. Also, magnetic nanoshells were synthesized by using block copolymer assemblies encapsulating magnetic nanoparticles as templates. Nanoshells of various surface morphologies such as spiky, blackberry, bumpy and blunt nanoshells were synthesized by varying the additives in the growth solution. These highly structured nanoshells possess high surface area and enhanced scattering properties compared to smooth shells. The enhanced optical properties together with the hollow morphology and straightforward synthetic procedure make the structured nanoshells an excellent system for sensing and biomedical applications.