One promising strategy to reconstruct bone defects relies on 3D printed porous structures. In spite of several studies having been carried out to fabricate controlled, interconnected porous constructs, the control over surface features at, or below, the microscopic scale remains elusive for 3D polymeric scaffolds. In this study, we developed and refined a methodology which can be applied to homogeneously and reproducibly modify the surface of polymeric 3D printed scaffolds. We have demonstrated that the combination of a polymer solvent and the utilization of ultrasound was essential for achieving appropriate surface modification without damaging the structural integrity of the construct. The modification created on the scaffold profoundly affected the macroscopic and microscopic properties of the scaffold with an increased roughness, greater surface area, and reduced hydrophobicity. Furthermore, to assess the performance of such materials in bone tissue engineering, human mesenchymal stem cells (hMSC) were cultured in vitro on the scaffolds for up to 7 days. Our results demonstrate a stronger commitment toward early osteogenic differentiation of hMSC. Finally, we demonstrated that the increased in the specific surface area of the scaffold did not necessarily correlate with improved adsorption of protein and that other factors, such as surface chemistry and hydrophilicity, may also play a major role.