Molecular dynamics simulations are used to study the structure and removal of prismatic dislocation loops during graphitization. The carbon models contain a mixture of screw and edge dislocations, and are created by self-assembly at high temperature. Four mesh-based analysis tools are used to track the time-evolution of the dislocation loops, providing insight into loop structure and allowing quantification of kinetics. We find that the loop structure is complex, being dispersed in three dimensions with alternating screw and edge components in multiple slip planes. Loop removal involves edge glide through kink formation and propagation, followed by a slower screw glide mechanism. All analysis tools yield similar activation energies, in the range of 2.9 ± 0.3 eV, consistent with recent experimental work by ourselves. Literature values for the kinetics of graphitization fall into two brackets, a lower range of 2.8–3.9 eV, and a higher range of 7.8–11.6 eV. This work supports the lower range and suggests that prismatic dislocation loops are the key defect removed during graphitization.