enable asp.net 4.0

I used vs 2010 to start a website using file system.  I already enable 4.0 framework from the application pool for the site.  Everything seems to work fine.

Now, I am trying to open the site using local IIS.  I get this message:

The ASP.NET 4.0 Web extension is not enabled on the Web server.  http://mywebsite is targeting ASP.NET 4.0.  Do you want to enable ASP.NET 4.0 on the Web server?

Action choices are: Yes, No, Cancel

What should I do?  What does that mean?  Should I stick to the file system to access my website?

Thanks.