The presence of bacterial biofilms is detrimental in a wide range of healthcare situations especially wound healing. Physical debridement of biofilms is a method widely used to remove them. This study evaluates the use of microfluidic jet impingement to debride biofilms. In this case, a biofilm is treated as a saturated porous medium also having linear elastic properties. A numerical modeling approach is used to calculate the von Mises stress distribution within a porous medium under fluid-structure interaction (FSI) loading to determine the initial rupture of the biofilm structure. The segregated model first simulates the flow field to obtain the FSI interface loading along the fluid-solid interface and body force loading within the porous medium. A stress-strain model is consequently used to calculate the von Mises stress distribution to obtain the biofilm deformation. Under a vertical jet, 60% of the deformation of the porous medium can be accounted for by treating the medium as if it was an impermeable solid. However, the maximum deformation in the porous medium corresponds to the point of maximum shear stress which is a different position in the porous medium than that of the maximum normal stress in an impermeable solid. The study shows that a jet nozzle of 500 μm internal diameter (ID) with flow of Reynolds number (Re) of 200 can remove the majority of biofilm species.