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The flow-induced displacement of thin flexural structures is commonly encountered in filtration applications. To account for the effect in mathematical modeling, arising fluid-structure interaction (FSI) models become much more demanding regarding both analysis and numerical methods compared to a rigid structure. Especially in the modeling of woven filters, the complex microstructure with thin yarns renders direct numerical approaches impractical. A FSI problem with non-stationary Stokes flow and a periodic structure, consisting of slender yarns in contact, is analyzed. A dimension reduction approach is employed, shrinking the three-dimensional microstructure to a two-dimensional, permeable Kirchhoff plate. Arising model parameters are three fourth-order stiffness tensors, attained from auxiliary mechanical problems on the filter’s periodic unit. The derived model is suited for efficient FSI simulations on the macro-scale. A complete numerical workflow is presented, comprising of a finite-element formulation for both micromechanical and macroscopic FSI simulations and an optimization framework for optimizing microscopic filter designs for a desired flow-induced filter displacement.