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Electron density irregularities in the ionosphere modify the phase and amplitude of trans-ionospheric radio signals. We aim to characterize the spectral and morphological features of E- and F-region ionospheric irregularities likely to produce these fluctuations or “scintillations”. To characterize them, we use a three-dimensional radio wave propagation model—“Satellite-beacon Ionospheric scintillation Global Model of upper Atmosphere” (SIGMA), along with the scintillation measurements observed by a cluster of six Global Positioning System (GPS) receivers called Scintillation Auroral GPS Array (SAGA) at Poker Flat, AK. An inverse method is used to derive the parameters that describe the irregularities by estimating the best fit of model outputs to GPS observations. We analyze in detail one E-region and two F-region events during geomagnetically active times and determine the E- and F-region irregularity characteristics using two different spectral models as input to SIGMA. Our results from the spectral analysis show that the E-region irregularities are more elongated along the magnetic field lines with rod-shaped structures, while the F-region irregularities have wing-like structures with irregularities extending both along and across the magnetic field lines. We also found that the spectral index of the E-region event is less than the spectral index of the F-region events. Additionally, the spectral slope on the ground at higher frequencies is less than the spectral slope at irregularity height. This study describes distinctive morphological and spectral features of irregularities at E- and F-regions for a handful of cases performed using a full 3D propagation model coupled with GPS observations and inversion.