Hi,
DSpace does not currently have a way to bulk remove anonymous access from every Community or Collection at once. If you truly want **everything** to be hidden, you may want to consider putting your DSpace site behind a firewall. DSpace is primarily built for open access, so it does assume that all Communities / Collections will be publicly available by default. You can change this setting Community by Community or Collection by Collection, but there's no way to do so in a bulk manner (you'd have to edit each individually)
We do however have a bulk access management tool to change the permissions of individual Items.
https://wiki.lyrasis.org/display/DSDOC7x/Bulk+Access+Management This can be used to quickly ensure that none of the content within your Communities or Collections can be downloaded or viewed while you work to modify the permissions of each Community and Collection.
Tim