In Southeast Alaska, extreme uplift rates are primarily caused by glacial isostatic adjustment (GIA), as a result of ice thickness changes from the Little Ice Age to the present combined with a low-viscosity asthenosphere. Previous GIA models adopted a 1-D Earth structure. However, the actual Earth structure is likely more complex due to the long history of subduction and tectonism and the transition from a continental to an oceanic plate. Seismic evidence shows a laterally heterogenous Earth structure. In this study a numeral model is constructed for Southeast Alaska, which allows for the inclusion of lateral viscosity variations. The viscosity follows from scaling relationships between seismic velocity anomalies and viscosity variations. We use this scaling relationship to constrain the thermal effect on seismic variations and investigate the importance of lateral viscosity variations. We find that a thermal contribution to seismic anomalies of 10% is required to explain the GIA observations. This implies that non-thermal effects control seismic anomaly variations in the shallow upper mantle. Due to the regional geologic history, it is likely that hydration of the mantle impact both viscosity and seismic velocity. The best-fit model has a background viscosity of 5.0×10^19 Pa-s, and viscosities at ~80 km depth range from 1.8×10^19 to 4.5×10^19 Pa-s. A 1-D averaged version of the 3-D model performed slightly better, however, the two models were statistically equivalent within a 2σ measurement uncertainty. Thus, lateral viscosity variations do not contribute significantly to the uplift rates measured with the current accuracy and distribution of sites.