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In case of a strong frequency modulated interference in a spread spectrum communication system, the interference can be effectively suppressed by applying a time-varying notch filter with its zero(s) placed at an instantaneous frequency (IF) estimate of the interference. In this paper, we present the use of a time-varying autoregressive model based IF estimator in such a scenario. We model the received signal with an autoregressive model whose coefficients are time-varying and modeled as a combination of a set of known functions of time. The IF of the interference is estimated from the model. It is demonstrated that this method provides superior performance compared to using a time-frequency distribution. The comparison reveals that the Wigner-Ville distribution peak based IF estimator suffers drawbacks such that its filtering gain is limited.