High-resolution imaging of optical resonator modes is a key step in the development and characterization of nanophotonic devices. Many sub-wavelength mode-imaging techniques have been developed using optical and electron beam excitation-each with its own limitations in spectral and spatial resolution. Here, we report a 2D imaging technique using a pulsed, low-energy focused ion beam of Li+ to probe the near-surface fields inside photonic resonators. The ion beam locally modifies the resonator structure, causing temporally varying spectroscopic shifts of the resonator. We demonstrate this imaging technique on several optical modes of silicon microdisk resonators by rastering the ion beam across the disk surface and extracting the maximum mode shift at the location of each ion pulse. A small shift caused by ion beam heating is also observed and is independently extracted to directly measure the thermal response of the device. This technique enables visualization of the splitting of degenerate modes into spatially-resolved standing waves and permits persistent optical mode editing. Ion beam probing enables minimally perturbative, in operando imaging of nanophotonic devices with high resolution and speed.