Indirect dynamic structural identification approach, often referred to as Vehicle Scanning Method (VSM), allows to estimate bridge modal parameters using data recorded from sensors directly mounted on a moving vehicle. This procedure has recently gained increasing attention due to its low cost and straightforward implementation [1, 2]. However, the complex nature of the vehicle-bridge interaction phenomenon poses some challenges to the accuracy of the method. In this regard, in this paper a novel procedure is proposed for the dynamic identification of bridges modal parameters based on the VSM, considering the effects of damping and road pavement roughness. Specifically, the Variational Mode Decomposition (VMD) method is herein used to determine the relevant Intrinsic Mode Functions (IMFs) and central frequencies from the recorded signal [3]. Further, the Natural Excitation Technique (NExT) is employed to generate equivalent free-decay modal responses from the decomposed signal. These are then used in combination with a noise-robust area ratio-based approach for the modal damping ratios estimation [4]. Finally, the mode shapes are evaluated by properly correcting the instantaneous amplitudes of each IMF considering the influence of the corresponding estimated modal damping ratio. Several numerical simulations are presented to show the validity of the proposed procedure and comparisons with the classical Hilbert Spectrum-based identification approach are employed to assess its reliability and improved accuracy.