We use helium ion microscopy (HeIM) to image the nanostructure of poly(3-hexylthiophene)/[6,6]-phenyl-C(61)-butric acid methyl ester (P3HT/PCBM) blend thin-films. Specifically, we study a blend thin-film subject to a thermal anneal at 140 °C and use a plasma-etching technique to gain access to the bulk of the blend thin-films. We observe a domain structure within the bulk of the film that is not apparent at the film-surface and tentatively identify a network of slightly elongated PCBM domains having a spatial periodicity of (20 ± 4) nm a length of (12 ± 8) nm.