Thank you for getting back to us.
From your post I get the impression that you are with the idea that Sitefinity manages physical ASPX pages. Sitefinity does not work that way - it creates the CMS pages and stores them in the DB, then whenever a pages is requested all its content and properties are pulled from the DB. You can add physical pages to your Sitefinity website sitemap, however you will not be able to change those pages through Sitefinity.
Although Sitefinity does not work with physical pages and directories it uses hierarchical system for the pages. So you can create pages and they can have subpages. Or create parent pages that have no content and only have children pages (the same as directory and pages within that directory). Now as Ivan has said you can use Sitefinity as any ASP.NET application. You can have your backend logic - not accessible to the public in the administration area of Sitefinity. Then you can have the CMS pages - the front end part of your application. You can use roles and permissions to define who gets to access what and what they can do about it.
I suggest that you take a look at the following resources so you gain a better understanding of the Sitefintiy CMS:
Sitefinity 3.6 new backend architecture
the Telerik team