Two-dimensional thermospheric wind fields, at both E and F region altitudes within a common vertical volume, were made using a Scanning Doppler Imager (SDI) at Poker Flat, Alaska, during a substorm event. Coinciding with these observations were F region plasma velocity measurements from the Super Dual Auroral Radar Network (SuperDARN) and estimations of the total downward and upward field-aligned current density from the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE). This combination of instruments gives an excellent opportunity to examine the spatial characteristics of high-latitude ionosphere-thermosphere coupling and how a process which is triggered in the magnetosphere (the substorm) affects that coupling at different altitudes. We find that during the substorm growth phase, the F region thermospheric winds respond readily to an expanding ionospheric plasma convection pattern, while the E region winds appear to take a much longer period of time. The differing response timescales of the E and F region winds are likely due to differences in neutral density at those altitudes, resulting in E region neutrals being much more "sluggish" with regard to ion drag. We also observe increases in the F region neutral temperature, associated with neutral winds accelerating during both substorm growth and recovery phases. Plain Language Summary At different altitudes in the polar atmosphere, how charged particles (the ionosphere) interact with neutral particles (the thermosphere) is of great importance. Primarily, this is because collisions between the two is the mechanism by which energy from the solar wind is ultimately deposited into the atmosphere, from the magnetosphere. Magnetosphere-thermosphere energy exchange drives auroral displays and contributes to heating in both the E region (altitudes between 100 and 130 km) and F region (altitudes between 150 and 300 km). The neutral atmosphere is significantly denser in the E region compared to the F region, so its interaction with the ionosphere at those different altitudes is quite different. In this study, we examined the E and F regions during a "substorm" event, which is a large, sudden injection of energy into the nightside ionosphere. We found that the velocity of neutrals in the E region reacted much more slowly than those in the F region, so that the conditions imposed on the E region before the substorm persisted during the substorm.