Nanostructured magnets have attracted great interest recently due to their new magnetic properties, which are completely different from those in the bulk, and their potential application in device miniaturization approaching the Tbit/in² recording density. In this thesis , we have fabricated sub-100 nm magnetic dots covering over 1 cm² area by electron-beam evaporation using self- assembled nanopores in anodized alumina as a shadow mask. Due to the large pattern coverage, and high degree of uniformity in both dot size and periodicity, magnetic measurements of such a dot array can be used to investigate the magnetism of a single dot of the average size. For Fe dots with a thickness of 20 nm, we find a transition from a single domain to a vortex state as the dot diameter is increased up to 60 nm. This single domain to vortex state transition has also been studied by the first order reversal curve method, which quantifies the magnetic phase fractions and distributions of vortex nucleation and annihilation fields. A magnetic vortex core size of 16±3 nm, which is close to or even smaller than the magnetic force microscopy (MFM) resolution, is measured by polarized neutron reflectivity measurements and verified by micromagnetic simulations. In addition to applications in magnetic memory systems and ultrasmall magnetic field sensors, magnetic nanostructures can also be used as the artificial pinning centers for superconducting vortices. We have observed asymmetric superconducting flux pinning effects with first matching fields above 2 kOe. Most importantly, we find that the properties of a magnetic vortex can be imprinted into transport properties of adjacent Al superconducting thin films, with dots' magnetic reversal events imprinted and magnified in the superconducting behavior. Chemical sensing and biosensing in porous alumina films, which exhibit more easily controlled pore sizes and higher chemical stability as compared to other porous materials, is studied using optical interferometry. The measured vapor capillary condensation and adsorption-desorption hysteresis is in qualitative agreement with theoretical models and a variety of simulations