Decisive advances in the fields 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 exploitation of the nano-structuring potential of a highly Focused Ion Beam as a tool, to overcome intrinsic limitations of current nano-fabrication techniques and to allow innovative patterning schemes 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 some advanced FIB processing schemes. These patterning schemes are (i) Ultra thin membranes as an ideal template for FIB nanoprocessing. (ii) Local defect injection for magnetic thin film direct patterning. (iii) Functionalization of graphite substrates to prepare 2D-organized arrays of clusters. (iv) FIB engineering of the optical properties of microcavities.