An ion beam imprinting system has been developed at Lawrence Berkeley National Laboratory recently. It is a useful tool to perform micromachining, surface modification, and ion doping etc. The principle of the imprinter is to directly transfer the pattern from the mask to the substrate. It is capable to produce multiple shaped ion beams simultaneously. Therefore it is much more efficient to do micromachining for large volume production than conversional focused ion beam system. Different shaped masks and diverse ion species have been tested both on conductors and insulators. Furthermore, the ion beam imprinter can transfer patterns not only onto a planar target but also onto non-planar surfaces, for example the outer and inner surfaces of cylinders. The imprinting technique can also be applied in three-dimensional micromachining, for example using cylindrical masks to fabricate the medical stents.