Adsorption and orientation properties of two different types of immunoglobulin molecules on derivatized and native mica surfaces were investigated using TM-AFM. The analyses included height measurements at two different pH values and a new technique, presented here as threshold analysis, which displays the outer mantle shape of an adsorbed protein. A major difference in preferential orientation is observed upon comparing the adsorption of the two proteins onto the different surfaces. The characteristics of both the adsorbed immunoglobulin and the surface are important for any preferential orientation of the adsorbed protein.