The drive towards controlling materials properties at nanometer length scales relies on the availability of efficient tools. Currently, high resolution ion beam processing is limited to direct-write techniques with mostly gallium ion beams, or the use of pre-structured masks. In this paper, several novel ion beam tools that have been developed at Lawrence Berkeley National Laboratory (LBNL) are reviewed: Maskless Micro-Ion-Beam Reduction Lithography system, Multiple Focused Ion Beam (FIB) system and ion beam imprinter, and a FIB/SEM dual beam system. With the availability of multicusp plasma ion sources, these ion beam tools can provide versatile ion beams in nanometer scale for future integrated circuit manufacturing, thin film media patterning, and micromachining