Assuming .Net framework is not installed. In that case follow the below step to enable IIS to run 32 bit ASP.Net applications.
Navigate to %WINDIR%\Inetpub\AdminScripts directory and run the adsutil.vbs script using the following command line
cscript.exe adsutil.vbs set W3SVC/AppPools/Enable32BitAppOnWin64 "true"
If you have .Net framework pre installed. Then after following the above step. Run the following command on the command line from the directory %WINDIR%\Mircosoft.Net\Framework\v2.0.50727
Now you can install 32 bit ASP.Net applications.
The above solution is for IIS 6.0 on Windows Server 2003 64 Bit.
Now I am going to explain how to achieve the same on IIS 7.0
As compared to all Microsoft products IIS 7.0 is also backward compatible. This is achieved through IIS 6.0 metabase compatibility and IIS 6.0 WMI compatibility. Installing this will make IIS 6.0 Default Application Pool on IIS 7.0. For installing these options, if IIS 7.0 is already installed, configure it using the Add Roles option under Server Manager.
From Server Manager, Select Web Server(IIS). Now from left pane click on "Add Rol Services". In the new windows, scroll down, to check "IIS 6 Metabase Compatibility" and "IIS 6 WMI Compatibility".
Now open IIS Manger. From left pane select "Set Application Pool Defaults...". Now under General, select "Enable 32-Bit Applications" as true.