Symmetry breaking (SB) of fluid-structure interaction problems plays an important role in our understanding of animals' locomotive and sensing behaviors. In this Letter, we study the SB of flexible filaments clamped at one end and placed in a spanwise periodic array in Stokes flow. The equilibrium state of the filament along the streamwise direction loses stability and experiences two-dimensional and then three-dimensional SBs as the spanwise distance increases, or as the filament rigidity reduces. For slightly deformed filaments, the viscous and pressure forces are commensurate, while for extremely deformed filaments the viscous force becomes dominant.