Arterial blood flow model may be used for diagnosis of hypertension, cardiac insufficiency, heart defects, coronary heart disease as well as origin and progression of arteriosclerosis. We present the designing guideline for object-oriented software systems of the above type, dealing with the high computational complexity and complicated data structures. The blood flow was modeled by Fluid Particle Model (FPM), extended to the case of non-linear flows. The wall dynamic was described by thin shell equation solved by Finite Elements (FE). Selected numerical scheme allows splitting of the numerical part of our system into two conjugated modules (FPM flow and FEM wall modules) and decreases computational complexity in comparison to the global FEM models. The core UML project components are the following: Vessel Geometry, Flow Calculations, Vessel Wall and Boundary Conditions. Object-Oriented architecture for the simulation software based on the FEM follows the bottom-up designing principle. The hierarchy of classes is distinguished - from the base class that expresses the single element through physical parameters and geometry to the type of FEM interpolation. Simulation results were consistently compared to medical ultrasound measurements performed on human arteries.