Are the data in the .nc file rasters? If so, I would open them separately and apply the raster mask of your choice to the data. You would be able to view the type of data in the File->Open As->Scientific Formats tool.

The data products are in .nc format, but when I use the open as -> scientific formats tool, the little icon next to rasters has a small red circle with a line through it & the bands of the flag rasters can't be added to the raster section on the right hand side of the dialog box.

As another potential solution, I exported the mask I wanted using the ESA SNAP software as a .xml file. However, ENVI won't read in the SNAP generated .xml. This is in ENVI 5.4.1, btw.

Thank you!

It would need to be a raster to be supported as a 'mask' in ENVI and a raster would not be stored in an XML. I am looking at a Sentinel-3 dataset that has the radiance bands in separate .nc files as well as the quality flags. However, in the Quality flags.nc, there is a 1D and 2D dataset where the 2-D data is of the same dimensions as the radiance data. This can be opened as a raster but not together with the radiance data. Are you able to open the file in this way?
I believe 1D scentific datasets support was added in ENVI 5.5, so that may be a limitation.

Hello! I can open the mask layer that way - the data then needs to be parsed to determine the value for each pixel for the different fields (land, water, cloud, ice, etc). MODIS flags operate the same way. I was just hoping there was a more straightforward approach - particularly if the .xml could be read like a shape-file or like a mask file. ESA's SNAP will parse the flag layers into specific masks, and then each mask can be exported as a single band raster, but in .xml format, which is not ideal. Oh well. Will work through it.

Thank you for your help, as always!