A patterned array consisting of a microstructured layer of octadecyltrichlorosilane (OTS) and (3-((2,4-dinitrophenyl)amino)propyl)triethoxysilane (DNP analogue) was assembled onto a Si wafer using the microcontact printing method. The microstructured, patterned support was imaged by AFM, using a bare Au tip, a hydrophobic alkyl mercaptan-functionalized Au tip, and a hydrophilic hydroxyalkyl mercaptan-modified Au tip. The lateral friction forces between the tip and the patterned surface are controlled by hydrophobic-hydrophobic and hydrophobic-hydrophilic interactions and eventually H bonds between the tip and the functionalized surface. The (3-((2,4-dinitrophenyl) amino)propyl)triethoxysilane domains of the microstructured surface act as antigens for the anti-dinitrophenyl antibody (anti-DNP-Ab). Interaction of the patterned support with the DNP-Ab solution yields an overall hydrophilic interface due to the association of the antibody to the entire support. Analysis of the adhesive and friction interactions between the Au tip and the DNP-Ab associated with the OTS and DNP analogue regions, and the roughness factors of the respective domains that include the DNP-Ab, enables us to conclude that the DNP-Ab associates nonspecifically to the OTS sites, while specific binding of the DNP-Ab occurs on the DNP antigen regions.