Scanning probe microscopy (SPM), a key invention in nanoscience, has by now been
extended to a wide spectrum of basic and applied fields. Its application to basic science led to a
paradigm shift in the understanding and perception of matter at its nanoscopic and even atomic
levels. SPM uses a sharp tip to physically raster-scan samples and locally collect information
from the surface. Various signals can be directly detected by SPM in real space with atomic or
nanoscale resolution, which provides insights into the structural, electronic, vibrational, optical,
magnetic, (bio)chemical and mechanical properties. This Primer introduces the key aspects
and general features of SPM and SPM set-up and variations, with particular focus on scanning
tunnelling microscopy and atomic force microscopy. We outline how to conduct SPM experiments,
as well as data analysis of SPM imaging, spectroscopy and manipulation. Recent applications of
SPM to physics, chemistry, materials science and biology are then highlighted, with representative
examples. We outline issues with reproducibility, and standards on open data are discussed.
This Primer also raises awareness of the ongoing challenges and possible ways to overcome
these difficulties, followed by an outlook of future possible directions.