We present a closed approach towards direct microstructuring and high precision prototyping with focused ion beams (FIB). The approach uses the simulation of the involved physical effects and the modeling of geometry/topography during milling while the ion beam is steered over the surface. Experimental examples are given including the milling of single spots, trenches, rectangles, and Fresnel lenses. Good agreements between simulations and experiments were obtained. The developed procedures can also be applied to other FIB prototyping examples.