Error when building website in VS2008

It is an error to use a section registered as allowDefinition='MachineToApplication' beyond application level. This error can be caused by a virtual directory not being configured as an application in IIS

I had recently upgraded to VS2008 from VS2005 and I would receive this error when trying to build a website that had also been upgraded. The error message was coming from the web.config line 29, however line 29 was a commented line in my current web.config. It turns out that it was looking at the web.config file in the backup folder that had been created during the upgrade process of the solution file. I removed the web.config file from the backup folder and the web site will now build.