High flux, low energy He plasma exposure is proven to nanostructure iron thin films over their entire thickness to a highly open structure with large surface area. From a large set of plasma exposure parameters, the ion flux, the surface temperature, and the plasma exposure time are found to be the most relevant parameters to process mechanically stable, nanostructured Fe thin films on brittle glass substrates. The nanostructure stays stable during oxidation. Different surface morphologies are found, depending on the location where the plasma plume interacts with the thin film. This method paves the way to a new direction in top down nanostructuring of thin films, which can be adopted for many functional materials in diverse applications that require a high ratio of active to projected surface area.