I mentioned this in reply to your other post, but I thought I'd mention it here as well:
ENVI itself does not currently have any batch mode routines for georeferencing MODIS data.  There is a feature request open for that.  If you contact support@ittvis.com, we can add your name to that request.
You may want to check out the MODIS Toolkit on our code library web site. Search in the ENVI category for MODIS, and you will find it.  It includes a routine that you can use to georeference MODIS data, with whatever input and output files you set up.  It doesn't automatically look in your input directory and loop throught all of the files there, but you can set that up yourself in your IDL code that calls the routine.
Peg