The introduction of mass-separated systems in the field of focused ion beams significantly increases the area of application in nanotechnology due to the availability of a broad spectrum of ions with the same advantages compared to classical Ga instruments. A short description of the configuration of a mass-separated FIB tool is given as well as the fundamentals of alloy liquid metal ion sources. Examples of application include patterned tailoring of functional surfaces and ioninduced phase transformation in thin layers, in particular the Si nanowire fabrication by FIB implantation and subsequent wet-chemical, anisotropic etching and the FIB lithography of thin ta-C films. Furthermore, the ion beam synthesis (IBS) of CoSi 2 nanostructures by Co-FIB writing and annealing, and the modification of surface morphology by various mono-and polyatomic projectiles in a broad energy and temperature range in different materials are described and discussed.