Authentication in Web.config.

Hi All,
          I am running into a problem.  I have ASP.net website which is using Form authentication in web.config and this ASP.net website is located in the root directory. There is another application which must use Window Authentication and it is located in subfolder under root. The problem is that when we try to run this Application under the root directory, it come out with error. Is there any configuration we need to do in IIS so that it will authenticate accordingly. 


Thanks in advance. 
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