It has become more important to shorten development periods of high performance computer systems and their LSIs. During debugging of computer prototypes, logic designers request very frequent LSI refabrication to change logic circuits and to add some functions in spite of their extensive logic simulation by several GFLOPS supercomputers. To meet these demands, an automated on-chip direct wiring modification system has been developed, which enables wire-cut and via-digging by a precise focused ion beam machine, and via-filling and jumper-writing by a laser CVD machine, directly on pre-redesign (original) chips. This modification system was applied to LSI reworks during the development of Hitachi large scale computers M-880 and S-3800, and contributed to shorten system debugging period by four to six months.