I have tried to delete a certain branch of my tree, but all I have succeeded in doing is unlinking the line but not permanently deleting all mentions of these people. I would very much like to do this as this line is the source of many matches, all of which are erroneous because I mistakenly included this line in my tree originally. Any help appreciated.
You can delete individual people. I assume you're working in Family Tree Builder. Find the person you want to remove, right-click on the card, click Person > Delete Person. Answer "Yes" to any warning that comes up. This should remove the card with any attached facts, notes, citations etc. Repeat this for every individual in the branch you want to prune (I hope there aren't hundreds!)