Hi Farshad, I understand the proces to deploy to a Azure VPS/VM, which is basically direct access to a server and configure ISAPI module on IIS. I would like to try to deploy to an Azure cloud service - web role. Azure manages the instance for you such as OS patches and security updates. The web role is basically IIS except that you don't need direct RDP access to configure the server. The web application (ISAPI, ASP.NET, etc.) is packaged and uploaded to the web role instead. I understand that ISAPI applications can be packaged in a cloud services package, just cannot figure it out and thought someone might have already been succeeded. Some links http://azure.microsoft.com/en-us/documentation/articles/cloud-services-how-to-create-deploy/
http://dotnetthread.com/articles/30-Choosing-between-Windows-Azure-Web-Sites-Web-Roles-and-VMs.aspx