The vortex matter in type-II superconductors continues to be a subject of great fascination in condensed matter physics. A longstanding theoretical and experimental problem is the identification of the ground state of the vortex lines in the presence of quenched atomic disorder which acts as random pinning centers. A possible edge contamination model has been proposed as a mechanism behind the seemingly contradictory experimental results for the ordered state of matter. This model could also explain the lack of universality for the peak effect behavior exhibited in samples with otherwise similar phase diagrams. Using a novel neutron diffraction technique, we report structural evidence for this edge contamination mechanism. This high-resolution method is used to study the fine structure of the vortex matter in a niobium crystal with a weak peak effect and a disordered zero-field-cooled vortex matter. We find this disordered state is metastable and that it can be restructured through a thermal cycling procedure. The results are explained in a strained lattice framework. We then perform Reverse Monte Carlo Refinements on our neutron scattering data and the possible vortex structures for our crystal agree with experimental results from an approach that combines spatial information with reciprocal space scattering. Having confirmed the existence of an edge contamination mechanism in this sample, we oxidize the surface in order to reduce the impact of the inhomogeneous surface barrier. By repeating our neutron diffraction measurements, we find that oxidation process has smoothed the magnetic field profile through the sample and improves the overall structural order of the zero-field-cooled vortex matter. On the other hand, the field-cooled vortex matter structure should be independent of any edge contamination effect but surprisingly, this scattering intensity in fact doubles after surface oxidation. This result suggests that there is another source of disorder in the niobium crystal that has been affected. We discuss our results in the context of the peak effect and Bragg glass models. Advisors/Committee Members: Ling, Xinsheng (Director), Kosterlitz, James (Reader), Mitrovic, Vesna (Reader).