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The aim of the study is to analyze the stability of the energetic particle modes (EPM) and Alfven Eigenmodes (AE) in Helitron J and LHD plasma if the electron cyclotron current drive (ECCD) is applied. The analysis is performed using the code FAR3d that solves the reduced MHD equations describing the linear evolution of the poloidal flux and the toroidal component of the vorticity in a full 3D system, coupled with equations of density and parallel velocity moments for the energetic particle (EP) species, including the effect of the acoustic modes. The Landau damping and resonant destabilization effects are added via the closure relation. The simulation results show that the n = 1 EPM and n = 2 global AE (GAE) in Heliotron J plasma can be stabilized if the magnetic shear is enhanced at the plasma periphery by an increase (co-ECCD injection) or decrease (ctr-ECCD injection) of the rotational transform at the magnetic axis (T0). In the ctr-ECCD simulations, the EPM/AE growth rate decreases only below a given T0 , similar to the ECCD intensity threshold observed in the experiments. In addition, ctr-ECCD simulations show an enhancement of the continuum damping. The simulations of the LHD discharges with ctr-ECCD injection indicate the stabilization of the n = 1 EPM, n = 2 toroidal AE (TAE) and n = 3 TAE, caused by an enhancement of the continuum damping in the inner plasma leading to a higher EP beta threshold with respect to the co- and no-ECCD simulations.