Static scaffold-based tissue engineering models fail to mimic the native microenvironment in terms of appropriate fluid flow and oxygenation conditions. Thus, only the outer layer of the cells remains viable, whereas the interior does not develop or eventually becomes necrotic due to hypoxia. Perfusion reactors, where medium is forced through the scaffold have been reported to be efficient for cell culture within porous scaffolds. However, most perfusion systems suffer from lack of homogeneity and their application is limited to only few scaffolds at a time. To overcome these obstacles, a multi chamber perfusion system was utilized, allowing culture of 40 3D scaffolds simultaneously, while monitoring and adjusting flow rate, temperature, pH and the dissolved oxidant content in real time. The ANSYS software was used in order to simulate the fluid flow regime and shear stress distribution under different operation modes. Our simulations so far indicated that bottom to top fluid flow is anticipated to result in a more homogenous flow and shear stress, compared to other operation modes. Based on these simulation tools, an optimal scaffold holding net was designed. Moreover, fluid flow velocity and other operational conditions will be further optimized to ensure both homogeneity of the flow and shear stress within all scaffolds and of precise control over oxygen level, and thus, better mimicking in vivo conditions. We intend to support our theory and simulation results with empirical experiments, testing which operation modes better mimic the functionality of in vivo tissue samples.