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The 3D nanostructure of organic materials plays a key role in their performance in a broad range of fields, from life sciences to electronics. However, characterising the functionality of their morphologies presents a critical challenge requiring nanometre resolution in 3 dimensions and methods that do not excessively distort the soft matter during measurement. Here we present scanning probe tomography using a commercial Pt-Ir coated tip and controlling the tip loading force to sequentially characterise and remove layers from the surface of a sample. We demonstrate this process on a sample exhibiting a polymer nanowire morphology, which is typically used for organic electronic applications, and present a tomographic reconstruction of the nanoscale charge transport network of the semi-crystalline polymer. Good electrical connectivity in 3D is demonstrated by directly probing the electrical properties of the inter-nanowire charge conduction.