Our preceding article [Phys. Rev. A 80, 012115] introduced a method to compute Casimir forces in arbitrary geometries and for arbitrary materials that was based on a finite-difference time-domain (FDTD) scheme. In this manuscript, we focus on the efficient implementation of our method for geometries of practical interest and extend our previous proof-of-concept algorithm in one dimension to problems in two and three dimensions, introducing a number of new optimizations. We consider Casimir piston-like problems with nonmonotonic and monotonic force dependence on sidewall separation, both for previously solved geometries to validate our method and also for new geometries involving magnetic sidewalls and/or cylindrical pistons. We include realistic dielectric materials to calculate the force between suspended silicon waveguides or on a suspended membrane with periodic grooves, also demonstrating the application of PML absorbing boundaries and/or periodic boundaries. In addition we apply this method to a realizable three-dimensional system in which a silica sphere is stably suspended in a fluid above an indented metallic substrate. More generally, the method allows off-the-shelf FDTD software, already supporting a wide variety of materials (including dielectric, magnetic, and even anisotropic materials) and boundary conditions, to be exploited for the Casimir problem.