I've not used Google drive, but if it works similar to other services, you have to use their interface to interact with the files. Thus any external software isn't going to work.
Depending on your connection speed and the amount of data involved, you could simply download everything, perform your cleanup, and then reupload it.
Depending on your connection speed and the amount of data involved, you could simply download everything, perform your cleanup, and then reupload it.