Here are some of the directories that are automatically created and may not be deleted:
Directories that contain your sites. Each of your sites is put in a separate directory. The name of the directory is the same as your site’s domain name. If you have more than one site, you will have several such directories. These are the directories where you will upload your .html files or any other files that you want to make accessible from the Internet. Each of these directories may contain their own /webalizer or /modlogan directories. Do not delete either of these directories! Your site is too valuable to lose at a touch of a button.
The Logs directory. It contains directories for every site with transfer log enabled. Each such directory contains its own set of log files that are required to write and read the data about all visits to your sites. Deleting the Logs directory will cause the loss of the web statistics accumulated in the course of your site operation.
The Virtual FTP directory. Its name is the dedicated IP address. This directory is created when you enable Virtual FTP Server and can be accessed by virtual FTP users to list and download its content. There are as many such directories as dedicated IP addresses. Deleting Virtual FTP directories will cause incorrect operation of Virtual FTP. However, you may harmlessly delete individual files in these directories.
The subdomain directories. When you make a subdomain, a new directory is created with the subdomain name as the directory name. If you delete a subdomain directory, internet visitors will get the 404 “File not found” error when attempting to access the subdomain.
The ssl.conf directory. This directory stores SSL pairs for all encrypted sites. Deleting the ssl.conf directory will result in incorrect SSL operation.