The cerebral thrombus or blood clot might cause cerebral stroke and even decease if the clot could not be dissolved within several hours after it was formed. We presented a treatment method of utilizing micro stirrer attached on the catheter tip. This paper presents the fundamental study on design of a micro stirrer for high effective dissolution. Based on the experimental results, the micro stirrer is analyzed by FEM. Using the FEM, new type of stirrer are evaluated. The obtained results of the in-vitro experiment and FEM analysis that the dissolution performance is influenced by the power into the fluid. Moreover, increase of the stirring area was tried by adjusting the input signal, and this effect was confirmed by the FEM analysis.