The applications of atomic force microscopy (AFM)in the MCT material and device processing are introduced. It can test the roughness of the polished material surface,the morphology of contact aperture and the surface morphology of epitaxial substrate. By selecting proper scanning parameters and probe,the morphology of the sample and the hole bottom topography of contact aperture can be obtained intuitively. Especially in the contact aperture testing,AFM has higher precision,stronger anti-interference ability,more intuitive and accurate results. According to the introduction of different samples,AFM plays an important role in the MCT material and device processing.