Check out the MSDN documentation for the ASP.NET IIS Registration Tool (Aspnet_regiis.exe) . There is an e and ea command line switch that you should use to clear it after the fact.
You can use Aspnet_regiis.exe to install and uninstall the system client side script, for example a script for client-side validation. Use the -c option to install the client script for the version of ASP.NET associated with this tool. (The script is installed in the Aspnet_client subdirectory of each IIS site directory.) To remove the client side of the script only for the version of ASP.NET associated with this tool, use the -e option. To remove the client side of the script for all installed versions of ASP.NET, use the -ea option.
(Emphasis added.)
Unfortunately, even the .NET 4 installer adds this directory, so cleaning will continue.
source share