Current commercial software tools implement turbulence models on computational fluid dynamics (CFD) techniques and combine them with fluid-structural interaction (FSI) techniques. There are currently a great variety of turbulence methods that are worth investigating through a comparative study in order to delineate their behavior on scaffolds used in tissue engineering and bone regeneration. Additive manufacturing (AM) offers the opportunity to obtain three-dimensional printed scaffolds (3D scaffolds) that are designed respecting morphologies and that are typically used for the fused deposition model (FDM). These are typically made using biocompatible and biodegradable materials, such as polyetherimide (PEI), ULTEM 1010 biocompatible and polylactic acid (PLA). Starting from our own geometric model, simulations were carried out applying a series of turbulence models which have been proposed due to a variety of properties, such as permeability, speed regime, pressures, depressions and stiffness, that in turn are subject to boundary conditions based on a blood torrent. The obtained results revealed that the detached eddy simulation (DES) model shows better performance for the use of 3D scaffolds in its normal operating regime. Finally, although the results do not present relevant differences between the two materials used in the comparison, the prototypes simulated in PEI ULTEM 1010 do not allow their manufacture in FDM for the required pore size. The printed 3D scaffolds of PLA reveal an elastic behavior and a rigidity that are similar to other prototypes of ceramic composition. Prototypes made of PLA reveal unpredictable variability in pore and layer size which are very similar to cell growth itself and difficult to keep constant.