You were on Cubase 5.5 if I recall, so when you go to export audio mixdown, you'll note there's a "channel batch export" checkbox in the top left corner and you can tick which channels you want to export. They will export based on the channel name and the prefix you choose on the right side of that menu. Cubase 6 gives you more options for the file naming.
I also recall some nuances with the export such as mono tracks going out as stereo if they have been routed to any stereo group, etc. There is a checkbox for mono export as well but I think it may be greyed out in 5 if there is any stereo routing.