The in-plane connectivity and continuity of lamellar-forming polystyrene-block-poly(methyl methacrylate) copolymer domains in thin films depend on the density and relative population of defects in the self-assembled morphology. Here we varied film thickness, degree of polymerization, thermal annealing time, and annealing temperature in order to engineer the defect densities and topology of the lamellar morphology. Assembly in thicker films leads to lower defect densities and thus reduced connectivity of the lamellar domains, which is considered in the context of the activation energies and driving forces for defect annihilation. Systems with smaller degrees of polymerization were also found to achieve lower defect densities and reduced domain connectivity. Most importantly, the relative populations of each type of defect were unaffected by the defect density, and these morphologies had similar long-range continuities. Controlling processing conditions such as thermal annealing time and temperature, in comparison, was ineffective at tuning the defect density of block copolymer lamellae because quasi-equilibrium morphologies were rapidly achieved and subsequently remained quasi-static. These results provide a framework for selecting the composition, degree of polymerization, and processing parameters for lamellar-forming block copolymers in thin films for applications that either require low defect densities (e.g., in the directed assembly of microelectronic architectures) or benefit from high defect densities (e.g., in network structures for transport).