In this work we present experimental and simulation analysis of the breakage and restructuring of colloidal aggregates in dilute conditions under shear. In order to cover a broad range of hydrodynamic and interparticle forces, aggregates composed of primary particles with two sizes, d(P)=90 and 810 nm, were generated. Moreover, to understand the dependence of breakage and restructuring on the cluster structure, aggregates grown under stagnant and turbulent conditions, having substantially different initial internal structures with fractal dimension d(f) equal to 1.7 and 2.7, respectively, were used. The aggregates were broken by exposing them to a well-defined elongational flow produced in a nozzle positioned between two syringes. To investigate the evolution of aggregate size and morphology, respectively, the mean radius of gyration, (R(g)), and d(f) were monitored during the breakup process using light scattering and confocal laser scanning microscopy. It was found that the evolution of aggregates' fractal dimension during breakage is solely controlled by their initial structure and is independent of the primary particles size. Similarly, the scaling of the steady-state < R(g)> vs the applied hydrodynamic stress is independent of primary particle size, however, depends on the history of aggregate structure. To quantitatively explain these observations, the breakage process was modeled using Stokesian dynamics simulations incorporating DLVO and contact interactions among particles. The required flow-field for these simulations was obtained from computational fluid dynamics. The complex flow pattern was simplified by considering a characteristic stream line passing through the zone with the highest hydrodynamic stress inside the nozzle, this being the most critical flow condition experienced by the clusters. As the flow-field along this streamline was found to be neither pure simple shear nor pure extensional flow, the real flow was approximated as an elongational flow followed by a simple shear flow, with a stepwise transition between them. Using this approach, very good agreement between the measured and simulated aggregate size values and structure evolution was obtained. The results of this study show that the process of cluster breakup is very complex and strongly depends on the initial aggregate structure and flow-field conditions.