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The direct femtosecond laser writing has been proved to be one of the most efficient techniques for micro-structuring of transparent materials, which can induce refractive index modifications to construct waveguide structures. In this work, laser-induced tracks with single-line configuration are formed inside the BK7 glass by using inscription of femtosecond laser pulses with 1 MHz repetition rate at wavelength of 1030 nm and 515 nm, respectively. The high-resolution confocal Raman spectra are obtained in the track regions to investigate the physical mechanisms of the modification. The results indicate that the specified regions inside the tracks induced by 1030-nm femtosecond laser expand and squeeze the adjacent area under certain writing conditions, leading to a refractive index increase in the core region. The 515-nm femtosecond laser brings out relatively more severe damage in comparison to the 1030-nm laser irradiation. A directional coupler structure has been fabricated by using the optimized writing parameters, showing a nearly balanced output with a ratio of 49.7:50.3 and an insertion loss of 1.36 dB for the single-line waveguide at 1064 nm.