Suspension thermal modes in interferometric gravitational-wave detectors produce narrow, high-$Q$ spectral lines that can contaminate gravitational searches and bias parameter estimation. In KAGRA, cryogenic mirrors are held by thick suspension fibers, designed to sustain such a low-temperature environment, which may further affect inharmonicity modes, fiber dimensions, and mechanical behavior compared to typical interferometers. As these modes remain a prominent source of narrowband contamination, we implement a Kalman filter to model and track violin lines, building on the methodology introduced in [1], and apply subtraction to KAGRA O3GK data. Using gravitational-wave template injections, we validate that the subtraction preserves matched-filter SNR while effectively suppressing line power. Comparisons of power spectral densities and residual analyses confirm that the method removes deterministic line contributions without introducing waveform distortions. This approach provides a cleaner strain channel for searches and parameter estimation and will become increasingly important for future low-temperature detectors with higher-$Q$ suspensions, such as the Einstein Telescope.

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• Gravitational wave detectors