Noise filtering in fluid dynamics enables stable, strongly-coupled molecular-continuum coupling despite potentially high thermal fluctuations. In this extended version of our conference paper “MaMiCo: Non-local Means Filtering with Flexible Data-Flow for Coupling MD and CFD” (ICCS 2021), we apply Non-Local Means filtering (NLM) in a novel space–time formulation to particle data. Our implementation in the Macro–Micro-Coupling tool (MaMiCo) features a flexible filter chain execution for HPC systems. We test it on 3D simulation data with multiple flow scenarios and continuum solvers, including a coupling to OpenFOAM. Our filtering results demonstrate that NLM not only has an excellent signal-to-noise ratio gain when extracting macroscopic flow information from particle ensembles, but also yields benefits for transient two-way coupling.