Large-eddy simulations of an SD7003 airfoil are conducted for an imposed plunging motion in order to induce a deep dynamic stall regime. Free stream flow parameters are set to Reynolds number Re = 60.000 and Mach number M = 0.1. Coherent structures are identified under the light of modal analysis via the multivariate empirical mode decomposition (EMD) and the multi resolution dynamic mode decomposition (mrDMD). The present study shows that the wavelet approach in the mrDMD does not fully compensate the errors in the frequency analysis related to rotational and translational invariances associated with vortex transport. Meanwhile the Hilbert-Huang transform applied to the intrinsic mode functions from EMD provides a more convenient way to identify the frequencies related to the coherent structures with negligible reconstruction error.