We propose a technique for formation of CoSi2 line structures on SiO2 films, which utilizes irradiation with 40 keV Si2+ FIB to the Co (14 nm)/Si (50 nm)/SiO2 (20 nm) stacked layer structures. Ion irradiation was performed at room temperature (RT) in order to prevent the thermal formation of cobalt silicide in regions without irradiation. After ion irradiation, unreacted Co layers remaining on the surfaces were removed by dipping the samples into the solution of HNO3:H2O2 = 1:3, and unreacted Si layers were removed by H3PO4 at 160 °C. The hot H3PO4 removes the deposited Si without etching the irradiated regions or SiO2 films. After the etching, the samples were heat treated at 700 and 900 °C for 20 min. As a result, cobalt silicide line structures were formed. The resistivity evaluated for samples heat treated at 700 and 900 °C was in agreement with that of CoSi and CoSi2, respectively. CoSi2 line structures with less than 200 nm width can be made by the procedure.