Problem in publishing the Web Application

Hi Friends,
                I have done finished web application project using IIS Server5.1. Now i am in client place to implement the project. Actually my project was in one seperate folder under the D: Drive. While clicking the publish button all code files are which are in outside folders are get converting. But the code files which are inside the folders are not get converting. 
Can anyone please guide me, How do Implement the web Application project in client side. How to publish the project.

Thanks in advance.
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