Planning of bypass surgery for patients with complex cerebral aneurysms is a very complicated task. It is important to take into consideration personal anatomy and hemodynamics and make additional investigations, but unfortunately, they don’t give a guarantee of good postoperative results. Recent medical imaging and computational fluid dynamics (CFD) can be helpful for the prediction of effectiveness of selected surgical technique. In the current research with the use of CT and PC-MRI data we applied computational modeling in order to make quantitative assessment of potential changes of blood flow distribution after the surgery. Virtual version of bypass surgery showed preservation of sufficient blood flow, what was confirmed with modeling results after operation. Moreover, successful verification with PC-MRI data in control sections was made. The research has shown that virtual planning with the estimation of blood flow changes can be introduced into clinical practice for simplifying and increasing efficiency of planning process.