'AFM' originates from English, specifically the phrase 'atomic force microscope' (or 'atomic force microscopy'), where 'atomic' meant 'of atoms', 'force' meant 'interaction force', and 'microscope' meant 'an instrument for viewing or measuring very small things'.

'AFM' was coined as an initialism after the invention of the atomic force microscope in 1986 (by Binnig, Quate, and Gerber); the letters A-F-M were taken from the full phrase and entered scientific literature and technical usage.

Initially it referred specifically to the physical microscope device; over time it came to be used for the broader technique ('atomic force microscopy') and, separately, as an initialism for unrelated organizations such as the American Federation of Musicians.