Bacterial adhesion on biomaterial surfaces is the initial step in establishing infections and leads to the formation of biofilms. In this study, silicone was modified with different biopolymers and silanes, including: heparin, hyaluronan, and self-assembled octadecyltrichlorosilane (OTS), and fluoroalkylsilane (FAS). The aim was to provide a stable and bacteria-resistant surface by varying the degree of hydrophobicity and the surface structure. The adhesion of Escherichia coli (JM 109) on different modified silicone surfaces was investigated by atomic force microscopy (AFM) and scanning electron microscopy (SEM). Mica, an ideal hydrophilic and smooth surface, was employed as a control specimen to study the effect of hydrophobicity and surfaces roughness on bacterial adhesion. AFM probes were coated with E. coli and the force measurements between the bacteria-immobilized tip and various materials surfaces were obtained while approaching to and retracting from the surfaces. A short-range repulsive force was observed between the FAS coated silicone and bacteria. The pull-off force of bacteria to FAS was the smallest among coated surfaces. On the other hand, heparin exhibited a long-range attractive force during approach and required a higher pull-off force in retraction. Both AFM and SEM results indicated that FAS reduced bacterial adhesion whereas heparin enhanced the adhesion compared to pure silicone. The work demonstrates that hydrophobicity cannot be used as a criterion to predict bacterial adhesion. Rather, both the native properties of the individual strain of bacteria and the specific functional structure of the surfaces determine the strength of force interaction, and thus the extent of adhesion.