We have investigated the effects of fabrication conditions on the properties of the interface-treated trilayer Josephson junctions. In the junctions, barriers are formed by ion milling, followed by annealing. We controlled the accelerating voltage for the milling process and the gas pressure for the annealing process. Josephson currents were observed in the junctions fabricated under various conditions. It was found that higher accelerating voltage contributes to the reduction of leakage paths in the barriers. However, clear dependence of the Josephson currents on the conditions was not observed in contrast to the results for the ramp-edge junctions.