hold shift or ctrl, highlight the entries that you do not want, and then click on any of the checkboxes you've highlighted... I feel bad for you knowing you've been clicking 100s of times :( ok...at least that is a temp solution. But i really hope Deluge will have some kind of folder/file structure...

I am wondering if there is any plugin that will allow you to do a bit more on file selection on magnet link download? Other bittorrent client will have some sort of filtering and file structure when you click on a magnet link/torrent file. On Deluge, you will see 100+ files flat listing without fold...