In this paper, specific emitter identification(SEI) problem has been investigated over fading channel. Different emitters are distinguished by the non-linear nature of the power amplifiers used by the emitters. This non-linearity is the fingerprint for the specific emitters. Based on this non-linearity SEI problem is solved. In this paper, we have considered several features like energy entropy, first and second order moment and correlation coefficient, which are calculated from the intrinsic mode functions(IMFs) obtained by using Variational mode decomposition(VMD). The SEI performance using EMD-EM2 method is compared with VMD-EM2 over fading channel, where entropy and first, second order moments are calculated from the Hilbert spectrum. The performance in terms of probability of correct identification for the second method is better than the first method for both single-hop and relaying case. Also the performance of VMD-CB is superior to VMD-EM2. © 2019 IEEE.