You cannot selectively Delete files, etc. from iCloud. If you select to have iCloud backup your "Documents", for instance, then ALL documents on your iPhone have to apppear in your iCloud account. The only way to remove ALL your documents from iCloud is to Delete them from your iPhone, in which case they will be deleted in iCloud, OR turn off syncing your "Documents" with your iPhone in your iCloud account. There is no way to just remove selected files from iCloud.