We report successful fabrication of submicron size intrinsic Josephson junctions (IJJs) using c-axis YBCO thin films of 800 nm thickness and Bi 2 Sr 2 CaCu 2 O 8 + d (Bi-2212) single crystal whiskers. The stacks of IJJs were fabricated by 3D focused-ion-beam etching method. First a microbridge was patterned in a required junction area by the normal direction etching. By tilting of the sample stage up to 90 o , two grooves on the bridge were etched from lateral direction in accordance to the required junction size. The 57-K-YBCO junctions did not show any degradation of critical current density (J c ) down to in-plane area of 0.5 μm 2 and show the current-voltage (I-V) characteristics of the collective switching transition from the zero voltage state to the resistive state. For Bi-2212 stacks smaller than 1 μm 2 , we identified some features of the charging effects on the I-V characteristics.