In this article, it is shown that focused ion beam (FIB) systems can be used to study the inner structure of flax fibers, the use of which as a reinforcing material in polymer composites still draws much interest from multiple disciplines. This technique requires none of the specific preparations necessary for scanning electron microscopy or transmission electron microscopy studies. Irradiation experiments performed on FIB prepared cross sections with very low Ga+ ion beam currents revealed the softer material components of fibers. Thus, it confirmed the presence of pectin-rich layers at the interfaces between the fibers of a bundle, but also allowed the precise localization of such layers within the secondary cell wall. Furthermore, it suggested new insights on the transition modes between the sublayers of the secondary cell wall.