Restored from backup with Migration Assistant - now have many folders at root level?

[cmarcus]

Here were my steps:

1. Boot MacBook Air from OS X retail DVD
2. Run Disk Utility and erase hard drive in MacBook Air (with zero overwrite, just to be sure : )
3. Install Mac OS X from DVD
4. Book MacBook Air from hard drive
5. Create user "test" during first boot
6. Log in as Test as run software update - install all updates
7. Restart
8. Log in as Test
9. Run Migration Assistant and migrate user "Cooper" from SuperDuper backup volume
10. Restart
11. Log in as Cooper
12. Delete user Test

Isn't this the correct procedure to "start fresh" with a clean OS X install?

Everything is working fine now, except I'd like those extra folders to be hidden - I hope I don't have to start that process over - it took hours!