Our research focuses on the fundamentals of magnetic nanoparticles that have very uniform sizes, as well as possible applications in magnetic storage and logic, permanent magnets, high frequency composites, and biomedicine. Monodisperse nanoparticles are synthesized by chemical methods and used as building blocks for self-assembly into arrays and for nanomasking pattern transfer into thin films. The collective magnetic behavior of the arrays has been studied using electron holography and Lorentz microscopy to image domains, and using polarized small angle neutron scattering to investigate the magnetization length scales within nanoparticles and their assemblies. We have demonstrated the ability of conductive atomic force microscopy to detect the state of a magnetic tunnel junction nanopillar, and switch it using a spin-polarized current.