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Methods for jammer rejection in spread spectrum communications, based on time-frequency representations, have been proposed in order to improve desired signal receiving performances. We also consider nonstationary jammer. The local polynomial Fourier transform (LPFT) is used to represent received corrupted signal. Time-varying filtering is implemented in this domain, having in mind that the LPFT is linear with respect to the signal. An order adaptive algorithm of the LPFT calculation is presented. Performance of the proposed nonparametric method is tested in the presence of linear and sinusoidal FM interferences in the noisy signal, without any a priori assumption about the jammer form. Results in terms of the bit error rate (BER) values are calculated, showing the achieved improvements. Since the first order LPFT is closely related to windowed modified fractional Fourier transform, procedure for an efficient optimization is presented.