The application of functional imaging tools and techniques on the molecular level enables investigators to characterize structures of biomolecules and interactions between biomolecules. The characterization of recognition events between biomolecules with atomic force microscopy (AFM) is a new methodology in biological research. Recent advances in the field of scanning probe microscopy especially atomic force microscopy have made it possible to discover the dynamic systems of molecular self-assembly and quantify the molecular forces between proteins. The interaction mechanisms between biomolecules were explored by many researchers to tackle broad-category initiatives of human diseases. This review overviews the advances in characterizing recognition events between proteins on the molecular level, specifically on antigen-antibody interactions and the aggregation of amyloid-beta peptides. AFM as an emerging approach for characterizing biomolecular interactions will also be highlighted. Furthermore, the potential and limitations of AFM for the measurement of single molecule interactions and the issues in analysis procedure will be discussed.