Zero-point electromagnetic fields were first introduced to explain the origin of atomic spontaneous emission. Vacuum fluctuations associated with the zero-point energy in cavities are now utilized in quantum devices such as single-photon sources, quantum memories, switches and network nodes. Here we present three-dimensional (3D) imaging of vacuum fluctuations in a high-Q cavity based on the measurement of position-dependent emission of single atoms. Atomic position localization is achieved by using a nanoscale atomic beam aperture scannable in front of the cavity mode. The 3D structure of the cavity vacuum is reconstructed from the cavity output. The root mean squared amplitude of the vacuum field at the antinode is also measured to be 0.92±0.07 V cm(-1). The present work utilizing a single atom as a probe for sub-wavelength imaging demonstrates the utility of nanometre-scale technology in cavity quantum electrodynamics.