What product did you use to get the marks out?
If the product you used left "micro marring" then use a milder product to remove the micro marring left by the more aggressive product.
For example you could remove the deeper defects with Meguiar's Ultimate Compound, then follow that up with ScratchX to remove the micro marring left by Ultimate Compound, then use SwirlX to remove the Scratch Micro marring if there was any left.
In my experience Technique makes a *huge* difference in the results you can achieve, so be sure to follow the directions and use even pressure on foam pads. Don't be afraid to use a little "passion" but don't apply all of your pressure using your finger tips.
If you have access to a DA polisher you can make short work of the swirls with a little practice