Decisive advances in the field of nanosciences and nanotechnologies are intimately related to the development of new instruments and of related writing schemes and methodologies. Therefore we have recently proposed the exploitation of the nano-structuring potential of a highly focused ion beam (FIB) as a tool, to overcome intrinsic limitations of current nano-fabrication techniques and to allow innovative patterning schemes that are urgently needed in many nanoscience challenges. In this work, we will first detail a very high-resolution FIB instrument we have developed specifically to meet these nano-fabrication requirements. Then we will introduce and illustrate an advanced FIB processing scheme that is the fabrication of artificial nanopores.