Scanning transmission ion microscopy (STIM) has been used in conjunction with channeling, to explore transmission channeling in thin epitaxially grown n-type silicon crystal. 1 MeV H + beams and 2.5 MeV α beams were used with beam currents of 0.1 fA focussed to spot sizes < 200 nm. Part of the sample was damaged in the channel and a random direction with the same beams focussed to a ~15 μm diameter spot size and current up to 2 nA. Theoretical calculations predict the general behaviour of collected energy spectra in both the random and the channel direction. The channeling STIM (CSTIM) technique can be 100% efficient, the analysis is achieved in a short time with negligible damage compared to backscattering channeling contrast microscopy (CCM), and it is capable of very high resolution (50 nm). These features can be successfully applied to the investigation of crystal damage and small size imperfections in samples transparent to the beam.