Numerical simulations of merging compact objects and their remnants form the theoretical foundation for gravitational wave and multimessenger astronomy. While Cartesian-coordinate-based adaptive mesh refinement is commonly used for simulations, spherical-like coordinates are more suitable for nearly spherical remnants and azimuthal flows due to lower numerical dissipation in the evolution of fluid angular momentum, as well as requiring fewer numbers of computational cells. However, the use of spherical coordinates to numerically solve hyperbolic partial differential equations can result in severe Courant-Friedrichs-Lewy (CFL) stability condition time step limitations, which can make simulations prohibitively expensive. This paper addresses this issue for the numerical solution of coupled spacetime and general relativistic magnetohydrodynamics evolutions by introducing a double fast Fourier transform (FFT) filter and implementing it within the fully message passing interface (mpi)-parallelized sphericalnr framework in the einstein toolkit. We demonstrate the effectiveness and robustness of the filtering algorithm by applying it to a number of challenging code tests, and show that it passes these tests effectively, demonstrating convergence while also increasing the time step significantly compared to unfiltered simulations.