This thesis presents an in-depth exploration of imperfections that can be found in self-catalysed III-V semiconductor nanowires. By utilising advanced electron microscopy techniques, the interface sharpness and defects at the atomic and macroscopic scale are analysed. It is found that a surprising variety and quantity of defect structures can exist in nanowire systems, and that they can in fact host some never-before-seen defect configurations. To probe how these defects are formed, conditions during nanowire growth can be emulated inside the microscope using the latest generation of in-situ heating holder. This allowed the examination of defect formation, dynamics, and removal, revealing that many of the defects can in fact be eliminated. This information is critical for attaining perfect nanowire growth. The author presents annealing strategies to improve crystal quality, and therefore device performance.