Helium ion microscopy (HIM) was applied to image an organic film filled into narrow trenches. The film was characterized to examine structural changes after the HIM helium ion irradiation comparing with a SEM electron beam irradiation. In the HIM case, the change was seen in a deep region of the film, while it occurred at the surface in the SEM case. This depends on penetration properties of helium ions and electrons to the material, and surface imaging of the film looks more realistic by the HIM than the SEM.