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.