Assuming you are hosting the application from yo web server...
For CGI to correctly run you need to ensure that the Website is allowing executables to be run.
If you go to the Website (Default Website) properties page you should see a section that allows u to specify what all is allowed to be run. i.e scripts or documents only or executables files too. For some perl CGI scripts you need to place them in the same folder as the html files themselves...
Another problem could be that the CGIapplication that u are running needs some changes in configuration to suit yo environment... check the READ ME file that came with the appl. they are normally very helpful