It is well known that endothelial shear stress affects occurrence of plaque in arteries. Lack of a method for measuring this physical quantity limits scientific understanding of this phenomenon. Application of numerical methods in this area has considerable amount of experimental verifications in terms of quantities that can be measured (velocity, pressure). On that basis we can rely on the results of endothelial shear stress calculations. The literature mainly documents the application of numerical methods to average geometries. However, arterial bifurcations are patient-specific. Moreover, occurrence of disease significantly complicates the geometry of the arteries and bifurcations. A multiblock concept provides the necessary geometrical flexibility and computational efficiency to generate patientspecific finite element models. For a particular class of problems different topologies of blocks are possible. This paper provides an overview of the possible block topologies required in finite element modeling using multiblock approach. In order to obtain accurate results of endothelial shear stress, two most general topologies are examined by numerical calculations. Favorable topology of the blocks is implemented in in-house software stl2fem.