Deep learning identification models have shown promise for identifying gas plumes in Longwave IR hyperspectral images of urban scenes, particularly when a large library of gases are being considered. Because many gases have similar spectral signatures, it is important to properly estimate the signal from a detected plume. Typically, a scene's global mean spectrum and covariance matrix are estimated to whiten the plume's signal, which removes the background's signature from the gas signature. However, urban scenes can have many different background materials that are spatially and spectrally heterogeneous. This can lead to poor identification performance when the global background estimate is not representative of a given local background material. We use image segmentation, along with an iterative background estimation algorithm, to create local estimates for the various background materials that reside underneath a gas plume. Our method outperforms global background estimation on a set of simulated and real gas plumes. This method shows promise in increasing deep learning identification confidence, while being simple and easy to tune when considering diverse plumes.