This article describes two algorithms for estimation of the optimal “system” parameters of time sequences (TSs) and frequency‐domain signatures generated in electromagnetic (EM) simulations. The time‐domain and frequency‐domain signal models are applied to data computed by the finite‐difference time‐domain (FDTD) method, and the method of moments, respectively. The FDTD method requires computation of very long TSs to accurately characterize the slowly decaying transient behavior of resonant structures. Therefore, it becomes critical to investigate methods of reducing the computational time for such objects. Existing methods in EM literature tend to use Prony‐based linear predictor‐type algorithms for modeling and extrapolating time‐domain data. These methods minimize a linearized “equation error” criterion that approximates the true nonlinear fitting‐error criterion posed by the estimation problem. In this article, we describe an efficient iterative method that minimizes the true nonlinear criterion and attains a significantly improved impulse response fitting over Prony's method, using fewer ARMA model parameters. The frequency‐domain state space method (SSM) presented in this article addresses the estimation of rational transfer function models from EM‐simulated data. The data are modeled in terms of complex sinusoids, whose amplitude and phase yield the decay/growth constants and the range, respectively, associated with discrete scattering centers. The model facilitates determination of key geometric and physical parameters of a circuit, antenna, or scatterer, which is an important first step in its design and optimization. Robust state space techniques, borrowed from linear systems theory, are applied to form the system matrix of the underlying microwave problem, whose complex eigenvalues, via signal compression and spectral decomposition, allow for the isolation of specific modal responses suited to calculation of the design parameters.