A two-dimensional-in-space mathematical model of amperometric biosensors with selective and perforated membranes has been proposed and analyzed. The model involves the geometry of holes partially or fully filled with an enzyme. The model is based on a system of the reaction-diffusion equations containing a nonlinear term related to the Michaelis-Menten enzymatic reaction. Using numerical simulation of the biosensor action, the influence of the geometry of the holes as well as of the filling level of the enzyme in the holes on the biosensor response was investigated. The numerical simulation was carried out using the finite difference technique. The calculation demonstrated that the effect of the filling level on the biosensor response decreases with decrease of radius of the holes.