On the Project Manager page, select the Topic you would like to delete.
You will see a list of the challenges you have within that Topic. Scroll all the way down to the bottom of the page. Click on 'Delete this Topic?'.
Do note that this action is irreversible. If you only want to take the Topic off the game temporarily to make edits and such, you can 'unpublish' the Topic instead. See: How do I 'publish'/'unpublish' a Project/Topic/Challenge?
Deleting a Topic will delete all the Challenges within them as well. If you would like to delete the Topic but keep the Challenges, you can move the Challenges to a different Topic, before deleting this Topic. See: How do I move one Challenge from a Topic to another