Optical microresonators have proven powerful in a wide range of applications, including cavity quantum electrodynamics1-3, biosensing4, microfludics5, and cavity optomechanics6-8. Their performance depends critically on the exact distribution of optical energy, confined and shaped by the nanoscale device geometry. Near-field optical probes9 can image this distribution, but the physical probe necessarily perturbs the near field, which is particularly problematic for sensitive high quality factor resonances10,11. We present a new approach to mapping nanophotonic modes that uses a controllably small and local optomechanical perturbation introduced by a focused lithium ion beam12. An ion beam (radius ≈50 nm) induces a picometer-scale dynamic deformation of the resonator surface, which we detect through a shift in the optical resonance wavelength. We map five modes of a silicon microdisk resonator (Q≥20,000) with both high spatial and spectral resolution. Our technique also enables in-situ observation of ion implantation damage and relaxation dynamics in a silicon lattice13,14.