Abstract Objective Polymer based materials used in the manufacture of extracorporeal circulation (ECC) circuit that is the main part of the heart lung machine used in cardiac surgery, poses the unavoidable inflammatory and coagulation reactions because of the contact with the tissue and biological fluids particularly the blood. The reason for these reactions may include chemical properties of the material used but the surface properties of the contact surface are also important. Atomic force microscopy (AFM) is useful method to analyze the surface morphology of a thin line and obtain information about the thickness, roughness and height asymmetries values such as the skewness and kurtosis of the line. The aim of the study is demonstrating the ECC circuits’ topographic features that hypothesized as one of the main reason for side effect reactions as inflammation and coagulation. Methods For this purpose, non-coated (n=3), heparine coated (n=3) and phosphorylcholin coated (n=3) ECC lines imaged by AFM and surface photographs, 3d topography, skewness and kurtosis of the sectional images and surface properties were evaluated at preoperative and postoperative. Results Atomic force microscopy images of the non-coated (n=3), heparine coated (n=3) and phosphorylcholin coated (n=3) ECC lines revealed that none of the circuit surface morphologies are enough for a biocompatible device. Conclusion Considering the biomaterial design approaches to date, although the influence of the chemistry of the substrate is certainly of high importance, micro/nanoscale topography on biomaterial surfaces is a promising new strategy and shows potential for improving blood compatibility.