To automate the deployment of a virtual machine scale set that uses the Windows Server 2016 Datacenter image and has web server components installed, you need to perform the following actions:
Modify the extensionProfile section of the Azure Resource Manager template. This section defines the extensions that are applied to the scale set virtual machines after they are provisioned. You can use the Custom Script Extension to run PowerShell scripts that install and configure the web server components. For more information, see Deploy an application to an Azure Virtual Machine Scale Set1.
Upload a configuration script. This is the PowerShell script that contains the commands to install and configure the web server components. You can upload the script to a storage account or a GitHub repository, and then reference it in the extensionProfile section of the template. For an example of a configuration script, see Tutorial: Install applications in Virtual Machine Scale Sets with Azure PowerShell2.