We present the application of digital filters to split the energy spectrum of an atomistic zone simulated with molecular dynamics into low and high energy components. After a brief background on digital filters, we describe the procedure used to select a cutoff frequency for the filters. Then, a one dimensional numerical model based on the Generalized Langevin Equation (GLE) is used to study the system dynamics. We tested both time and spatial filters for the frictional term in GLE. Our results demonstrate that spatial filters are better than time filters to perform a selective damping within a molecular dynamics zone. Two dimensional examples validating our approach are also presented. Spatial filters should thus be favored in finite-temperature direct-coupling methods between molecular dynamics and finite elements.