In recent years, the atomic force microscopy (AFM)-based techniques have gained popularity in biomedical applications. Different modes such as contact, no-contact, and nanoindentaiton of an AFM can be very useful to understand nanoscale phenomena of cancerous cells. In particular, morphological and phase contrast images, and nanomechanical data obtained from an AFM can provide a better understanding on the nature, strength and progression these cells, and treatment measures can be adopted based on the diagnoses results. This paper provides an overview of different AFM-based scanning modes and its prospects in biomedical applications based on an extensive review of existing literature available in public domain. Outcomes of this study are expected to be beneficial for researchers and medical professionals in getting familiarized with the AFM technologies and their applications as novel diagnostic tools.