How to delete bookmarks in NERDTree (Vim)?

Put your cursor over the bookmark you want to delete and hit shift-d (i.e. capital D).

If you hit ? question mark while in the NERDTree window you'll find the docs for this. Search for "delete".

You can use NERDTree command: :ClearBookmarks [<bookmark-name>]

or

Ctrl-w move your cursor to NERDTree window, type B if your bookmark table is not displayed, select the bookmark you want to delete in the bookmark table, type D (i.e. shift + d)

or

vim ~/.NERDTreeBookmarks then delete the line which you want to delete

Read the documentation :h NERDTree carefully