Normally to remove a file or folder from Time Machine, you would open Time Machine, highlight the file or folder, and then choose Remove from Backup in the options pull down.

But to do this with an invisible directory in the Finder by using Go -> Go to Folder… (command-shift-G) and enter the path. Once it’s showing, Enter Time Machine and follow the steps here.

Note: you can delete the folder you’re looking at (instead of a file/folder within it) by righ/control-clicking in the Finder window in Time Machine and selecting the Delete All… option with its name there.