For Josephson junctions using a narrow groove on a substrate etched by a focused ion beam (FIB), there is a strong relation between junction properties and groove shapes. We have developed the FIB milling method which has flexibility to produce a variety of different groove shapes. V-shape grooves with different sizes (width=215-594 nm, depth=27-92 nm) have been formed with the same slope angle on the MgO  substrate. The top surface profile of the 300 nm thick YBa/sub 2/Cu/sub 3/O/sub 7/ (YBCO) film had the same V-shape as the grooves on the substrate, but the YBCO groove widths were 110 nm narrower than the FIB groove widths. The 3 /spl mu/m width junctions fabricated on these grooves showed RSJ type I-V curves without exception and had the average of critical current (Ic) values of 0.520 mA at 4.2 K.