Full characterization of the three-dimensional structures resulting from the directed self-assembly (DSA) of block copolymers (BCP) remains a difficult challenge. Transmission electron microscope (TEM) tomography and resonant soft x-ray scattering have emerged as powerful and complementary methods for through-film characterization; both techniques require samples to be prepared on specialized membrane substrates. Here we report a generalizable process to implement BCP DSA with density multiplication on silicon nitride membranes. A key feature of the process developed here is that it does not introduce any artefacts or damage to the polymer assemblies as DSA is performed prior to back-etched membrane formation. Because most research and applications of BCP lithography are based on silicon substrates, process variations introduced by implementing DSA on a silicon nitride/silicon stack versus silicon were identified and mitigated. Using full-wafers, membranes were fabricated with different sizes and layouts to enable both TEM and x-ray characterization. Finally, both techniques were used to characterize structures resulting from the DSA of lamella-forming BCP with density multiplication.