A study involving the removal of blood clots in cerebral vessels by aspiration thrombectomy is presented. A robust design for the distal end geometry of a catheter is obtained that, together with adequate suction conditions, could avoid potential damage in the artery or fragmentation the thrombus. The optimization process of the parameters is undertaken by a Design of Experiments (DOE) that has been prepared based on Robust Design theories. In particular, 27 experiments are run for one factor at 9 levels (catheter geometry) and up to 9 factors at 3 levels. The experiments are formulated with virtual models that are solved with computing tools. Co-simulation between Computer Fluid Dynamics (CFD) and Finite Elements Method (FEM) structural analysis was used to obtain the suction conditions and the behavior of the blood clot during the intervention process. By comparing the results of the 27 experiments, the highest values of the suctioning force are obtained for a hole pattern based catheter design, that also gives the lowest risk for clot damage (based on the stress value obtained). Direct aspiration and designs based on conical catheter distal ends, give less robust solutions (results are not stable when the conditions of the environment change). Our study investigated the distance between the catheter and the clot, and it was noted that if the catheter was far from the clot, the suction generated a vessel narrowing and consequent potential damage. Up to 90 kPa could be applied when suctioning at a maximum distance equal to the diameter of the vessel between the distal end of the catheter and the proximal end of the clot. A maximum suctioning force of 0,514N was achieved without damage to the artery or the clot. This research enables us to determine and use the most representative parameters and geometries to be tested in in-vitro and in-vivo experiments. In this virtual study, hypothesizes are assumed with regard to the material properties, but the robustness of the design process allows to expect similar results in future in-vitro and in-vivo tests.