The potentialities of the atomic force microscopy (AFM) make it a tool of the undeniable value for the study of biomolecule samples. One of the main steps for the application of atomic force microscopy to the study of proteins has been the self-assembled monolayers (SAMs). The methods of physical adsorption and chemical modification are utilized to immobilize proteins to substrates efficiently. SAMs play an important role in protein immobilization. Membrane proteins need especial immobilization procedures in order to maintain their biological activities in vitro. This review proposes some fundamental methods of protein immobilization for AFM study.