You need to do a complete  database restore.

However, it isn’t quite as bad as it may seem. You can restore  to a different IIS virtual server  and different databases. This then allows you to extract the documents  you are after & manually put them back into the original portal.

Using CLI you can also do the more granular site level backups (not the
entire portal) yielding to faster restore  with less excess baggage.

You can also have versioning enabled on Doc libraries which can be viewed as
"hot backup", means previous version of the docs could be replace the
deleted doc instantly.