Darren,
Depending on what you're working on, I'd remove the clear part from the model, strip the paint (carefully!!), polish the part as best you can, dip the thing in Future, then start painting again.
This time, for a masking agent, use Bare Metal Foil - it's easy to apply, works very well, and is easy to remove.
What have you scratched - a/c canopy, car windows - what?
Cheers
LeeTree