The atomic force microscope (AFM) is the subject of numerous papers and reports and is full of promises for nanoscience and nanotechnological applications. Pharmaceutical and biopharmaceutical studies using AFM have been functionalized during last two decades. Since, its invention in 1986, the number of published articles has considerably increased. Owing to its unique ability to not only image but also probe mechanical and chemical properties with sub nanometer resolution under physiological condition made it an attractive tool. It can be relatively easily operated in fluids, and thus experiments can be conducted under nearly physiological conditions, which pace its numerous applications in biological problems. In the field of pharmaceutical sciences, AFM presents a unique opportunity to study a variety of phenomena at the cellular and sub cellular level, down to individual (macro) molecular complexes. These advantages of AFM allowed the advent invention of fabrication variables, dynamic processes, drug structure-function relationships, in real time. This article reviews the study of AFM to investigate the crystal growth, polymorphism, particles, granules and coating morphology of solid dosage form for optimization of pharmaceutical behaviors. It also highlights the in situ biopharmaceutical investigation of cell-macromolecular surface, drug-drug, drug-cell, drug-DNA, DNA-protein, drugenzyme and antigen-antibody interactions, and disease mechanisms to understand the better physiological mechanisms associated with disease to rationalize the drug design and development.