If the mask is not available for selection, this usually means that the mask and the image you are trying to apply it to do not have the same dimensions (in samples and lines). Which image did you use to create the mask? Did you layer stack the images (MS and thermal) and if so, did you create the mask from the stacked images? If you stack the images, they will likely have different spatial dimensions than the original images. So in this case, the mask would be needed to be created from the stacked bands.

I am using the *_MTL_Multispectral dataset as the input image, and the "fmask" file (file created from the cloud mask of the stacked images) as the mask. I entered the image stack for both the "Multispectral TOA Reflectance Raster" and the "Brightness Temperature Raster" prompt. I have tried the procedure both ways - with the stacked images and as separate reflectance and brightness temperature rasters, and am still having trouble getting the fmask file to show up when I attempt to apply the cloud mask. The fmask file shows up in the input file, but not in the available files in the "mask selection" dialog. When I browse to the file and select it, it also does not appear in the dialog menu. Lastly, I've attempted to export the fmask file as a tiff, and though I am able to export it as a tiff, I am still unable to use it as a cloud mask. Thanks in advance for any additional suggestions!

I found the issue and it is a bug. In the current version of ENVI (5.3.1 or SP1), there is a bug that does not allow the classification image to be selected as a mask when using the File->Save As option. This will be fixed in the next release. For now, you can use Apply mask from the toolbox. Select the MS image and the FMask classification image as the mask. The output masked areas will be 0 as the default value.

Thank you for your assistance! I will use the "Apply Mask" tool until the next release.