We have tracked the mobility, approach, and annihilation of defects in cylinder-forming diblock copolymer thin films on nanopatterned substrates using high-temperature and in situ time-lapse atomic force microscopy. This has been accomplished by visualizing two isolated defects and studying their approach and hence interactions. Here we used lithographed channels to template and orientationally align cylindrical diblock domains macroscopically and with low defect density. Dislocation pairs annihilate through climb and glide motion, where climb is defined as a dislocation displacement along the diblock domain stripes, and glide is defined as dislocation motion across the stripes. Defect mobility via climbing motion is observed to be faster than glide excursions. The diffusion coefficients parallel (D-par) and perpendicular (D-perp) to the striped nanodomains have been determined; mobility along the cylinder direction is approximately 1 order of magnitude larger than that across the cylinders. Diffusion activation energies of both motions have been extracted from variable temperature measurements of defect mobility. Additionally, disclination pairs have been observed to annihilate by emission of dislocations and the topological switching of disclination cores. These measurements of single-defect mobility in otherwise perfected nanodomain regions allow for unusually precise determination of defect mobility and energetics for both dislocation and disclination pairs in nanoconfined polymer thin film systems.