Clay will also remove scratches. It will remove high spots and fill in low spots. Clear coat still acts as a liquid. Heck even glass can be cleaned as it reacts as a liquid too. On glass you use OOO wire pad and paste.
I have detailed many vehicles that had scratches before clay.
Shuffler, what you are seeing is more likely due to the lubricant used with the clay. Most of the lubricants have a water based polymer included to help with the lubrication process. Check your lube. It is the likely reason you are seeing swirl marks being filled.
I have been painting and detailing cars for over 40 years. I was lucky enough to live across the street from a custom car builder who was good enough to teach me a lot of tricks with paint.
Here is a really good article on clay use and its impact.
http://www.hotbodywax.com/ClayBars.html<snip>
Roy ever deal with blanket marks in paint? Had a hudson hornet that was stored for too long with just a blanket to protect it...... you could see the weave of the blanket in the paint,but it was the old school enamel paint.
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Have had to deal with a few of those.
Side note: If you are going to cover your car for an extended period of time, then clay the paint, and apply a good sealant to it, not wax!
Make sure you use a car cover which also reflects UV.
Then, before you put the cover over it, take Saran wrap and cover all the horizontal surfaces, making sure to smooth the wrap out. Then affix the cover. You can also use the Saran wrap trick under fender covers when you work on your car.
Now to the enamel paint.
First, test the enamel to see if it is baked or sprayed. You do this by wetting the end of a toothpick and, using an obscure place, attempt to mar the surface of the paint by dragging the tip of the toothpick over it. If there is a visible mark left, then the paint is sprayed on. If it is not marked, then it is baked on.
Whether of not it is painted or backed makes a big difference in how you approach the removal of surface embedded marks. In both cases, there is an abundant amount of paint on the surface to work with.
It if is baked:
You can use a light polishing compound to remove the surface marks. Be sure to clean and clay first. A good random orbital polisher would be advised.
If it is painted, not baked on:
This is a bit trickier as the paint is a lot softer. Instead of using a polishing compound, get a soft pad for your random orbital polisher and use the same lubricant you use for claying and buff it out, using very light pressure with the buffer. You will need to change the pad many times. DO NOT let build up on the pad occur!!!
Good luck.