High-fidelity operation of quantum computers requires precise knowledge of the physical system through characterization. For motion-mediated entanglement generation in trapped ions, it is crucial to have precise knowledge of the motional-mode parameters such as the mode frequencies and the Lamb-Dicke parameters. Unfortunately, the state-of-the-art mode-characterization schemes do not easily render the mode parameters in a sufficiently accurate and efficient fashion for large-scale devices, due to the unwanted excitation of adjacent modes in the frequency space when targeting a single mode, an effect known as the cross-mode coupling. Here, we develop an alternative scheme that leverages the degrees of freedom in pulse design for the characterization experiment such that the effects of the cross-mode coupling is actively silenced. Further, we devise stabilization methods to accurately characterize the Lamb-Dicke parameters even when the mode frequencies are not precisely known due to experimental drifts or characterization inaccuracies. We extensively benchmark our scheme in simulations of a three-ion chain and discuss the parameter regimes in which the shaped pulses significantly outperform the traditional square pulses.