I have asp.net mvc 4 web application project on my server in IIS Directory.
I have created collection and added my project.
But mtf copied my project into another directory does it possible to add my application without copying it and to work tfs with same directory
Yes, like mentioned above you can change the local workspace mapping to match the folder structure on your machine. You go to Source Control Explorer > Workspace > Workspaces > Edit. Then map the source location to the local path and it will be in sync.
If you are using this server as a developer PC, I would recommend keeping all source control under a single folder like c:\tfs and then use a Virtual Directories or IIS Express to host the sites.
Mike