Applications of diamond and amorphous carbon films in micro-mechanical and sensor elements often require formation of submicron size patterns. A focused beam of 50 keV Ga+ ions was used in this work to fabricate sub-100-nm patterns in bulk diamond, CVD diamond and amorphous carbon films. The influence of the focused ion beam (FIB) parameters and ambient gas on the sputtering yield, surface morphology and structure modification of these materials war. studied using ion microscopy, atomic force microscopy (AFM), measurements of electric resistivity and Raman spectroscopy. Detailed results on FIB gas assisted etching (GAE) are reported. GAE processes with NH3+Cl-2 and XeF2 were found to enhance the sputtering yield of diamond and ta-C films 4-7 times. The electric resistivity of FIB GAE patterned material is almost independent on the ion dose and it is of 1-2 orders of magnitude higher when compared to the electric resistivity of non-assisted FIB patterned material.