Optical nonlinear Fourier transform-based communication systems require an accurate estimation of a signal's nonlinear spectrum, computed usually by piecewise approximation methods on the signal samples. We propose an algorithm, named successive eigenvalue removal, to improve the spectrum estimation of a multi-soliton pulse. It exploits a property of the Darboux transform that allows removing eigenvalues from the nonlinear spectrum. This results in a smaller pulse duration and smaller bandwidth. The spectral coefficients are estimated successively after removing the eigenvalues of a signal. As a beneficial application, we show that the algorithm decreases the computational complexity by iteratively reducing the pulse duration.