I accidentally clicked mark all as trade one evening on my Magic collection and I want to remove all and start selectively marking my cards to trade. How can I do this without starting all over again or going through one by one...

If you use the "Remove Everyhting" option in your tradelist, all the cards are removed from the tradelist, but they will still be listed in your inventory.

By the way, before doing big changes such as this it helps if you first export your inventory as csv as a backup.