I would assume they would be clear.
Either way, I'm guessing you would want to replace them. They most likely emit light that has the yellowish tint that all incandescant bulbs do. Since it is, as far as I know, illegal to have clear tail lights, I would look for some red LED "bulbs" which fit into the pre-existing socket, or get some bulbs, remove the glass and filament, and use that to wire up some LEDs.
The other thing you might be talking about are the rear lights on the bottom, sides of the rear bumper? I would also assume they would have clear bulbs.
__________________ 2006 4.6L V8 Mustang GT - - Black with soon-to-be Red Over-The-Top and Side Stripes - - Black Leather Interior - - Interior Upgrade Package - -Shaker 1000 - - Red Calipers
R.I.P.: 6-26-2007 to 6-18-2008 at 11:58am:
2007 4.0L V6 Mustang - - 5-speed - - Black w/ White Racing Stripes | 
Rear bumper light question, 2007 Mustang GT/CS 
