What you will want to do is use ENVI's Build Mask tool to build a mask image from your original thermal bands. You will want the areas that you eventually want to ignore in the mosaic to be masked (display as black), and the areas with real data values to be unmasked (display as white). Then you can take this mask image and use ENVI's Apply Mask tool to convert the "atmospherically corrected" non-data pixels to some constant pixel value that identifies them as background. Then in the mosaicking tool, you can specify this pixel value as the data value to ignore. - Peg Exelis VIS