Fluid flow through a bone scaffold structure is an important factor in its ability to build up a living tissue. Permeability is often used as a measure of a structure's ability to allow for flow of nutrients and waste products related to the growth of new tissue. These structures also need to meet conflicting mechanical strength requirements to allow for load bearing. In this work, the effect of different bone structure morphologies on permeability were examined both numerically and experimentally. Cubic and hexagonal based three dimensional scaffold structures were produced via stereolithography and 3D printing techniques. In particular, porosity percentage, pore size, and pore geometry were examined. Porosity content was varied from 30% to 70% and pore size from 0.34 mm to 3 mm. An adapted Kozeny-Carmen numerical method was applied for calculation of permeability through these structures and an experimental validation of these results was performed via a standard permeability experimental testing set-up. From the results it was determined that increased permeability was provided with the cubic rather than hexagonal structure as well as by utilizing the larger pore size and higher levels of porosity. Stereolithography was found to be the better processing technique, not only for improved micrometer scale dimensional accuracy reasons, but also due to the increase wettability found on the produced surfaces. The appropriate model constants determined in this work will allow for analysis of new alternate structure designs on the permeability of rapid prototyped synthetic bone structures.