This chapter introduces atomic force microscopy (AFM) as an important tool for protein nanotechnology. A short review of AFM-based imaging, mapping, and spectroscopy of protein samples is given. AFM imaging of β-lactoglobulin nanofibrils in air is demonstrated. Basic concepts of AFM are described. Protocols for β-lactoglobulin nanofibrils and multiwall carbon nanotubes (MWCNT) samples preparation are defined. The operation of the microscope is described using MWCNT and the NanoScope E instrument in contact mode as an example. Nanostructure manipulation based on AFM nano-sweeping is demonstrated.