• Machining performance of the FIB irradiated tool was improved by the heat treatment. • Gallium ions were removed by the proposed heat treatment. • Wear resistance of the FIB affected area was inferior to the non-irradiated area. Tool shape is an important factor determining the shape and accuracy of machined areas in ultra-precision machining. Use of a focused ion beam (FIB) is an effective means to fabricate micro- to submicro-scale tool shapes. However, ion irradiation causes doping and defects in the tool that reduce tool performance. To use FIB machining on a single-crystal diamond tool without degrading tool performance, a combination of 500 °C heat treatment and aluminum deposition was used to remove gallium (Ga) ions induced by ion irradiation. The method was evaluated through machining experiments that showed that irradiation of Ga ions causes work materials to adhere to the tool surface. This adhesion and the resulting rapid tool wear were reduced by heat treatment. The proposed method also improved the transcription ability and wear resistance of the tool so it was capable of producing a surface quality better than or equal to that produced by non-irradiated tools, even over long cutting distances.