Problems frequently encountered in kidney malfunction include abnormal fluid levels in the body, increased acid levels, abnormal levels of Urea, Glucose, Endothelin, β2-Microglobulin and Complement Factor D. Parameters characterizing the structure of dialyzers are very important because they decide overall clearance of toxin molecules and at the same time should allow retaining useful molecules in the blood. In this paper, a cross sectional image of the dialyzer membrane with details of the porosity is presented. A multilayered membrane model with different porosity for each layer, describes the actual structure of Polyflux 210H membrane. This model is developed using Finite Element Software—COMSOL Multiphysics 4.3. A blood flow with substances like—Urea, Glucose, Endothelin, β2-Microglobulin, Complement Factor D and Albumin is introduced. For a certain blood flow rate, the toxins diffuse through the membrane and on the other side of the membrane a dialysate flow removes the toxins. Here, different parameters, such as flow rate of blood and dialysate, length and radius of the fiber are changed to simulate how these changes affect toxin clearance and the removal of useful molecules.