We report on the morphological study of focused ion beam (FIB) milling of both sputter-deposited and single crystal (0 0 0 1) ZnO substrates. The surface roughness and the FIB induced sputtering yield were measured as a function of the ion dose and angle. Smoothing effect of rough films deposited by sputtering has been found at low ion doses. FIB milling at non-normal incidence produced roughness increase and the formation of ordered terraces on (0 0 0 1)-oriented sputtered ZnO. Conversely, surface roughness and FIB yield on single crystal ZnO substrates is basically unaffected by ion dose and milling angle.