Highly Focused Ion Beams (FIB) are used to produce in one step large quantities of solid state nanopores drilled in thin dielectric films with high reproducibility and well controlled morphologies. We explore both the production of nanopores of various diameters and study their applicability to different biological molecules such as DNA, or folded and unfolded proteins, and then we compare their transport properties. We also report on the translocation of Fibronectin which an original experiment made possible is using the methodology described in this article.