Focused ion beam milling is used to fabricate micron and submicron scale patterns in sintered silica colloidal crystal films. Rectangular cavities with both solid and porous boundaries, fluidic channels, and isolation of a small number of packed spheres are patterned. The ion beam can pattern sintered films of individual submicron size spheres and create patterns that cover up to 40 mu m in less than 15 min. The experiments in this work indicate that the amount of redeposited material on the surface of a milled cavity determines whether the surface will be porous or solid. FIB direct patterning has applications in colloidal crystal based lithography, integrated photonic devices, optofluidic devices, and micrototal-analytical systems.