In some cases you may want or need to change the version of .NET that a particular web application directory uses. Normally this is done via the ASP.NET tab on the IIS properties page for the web app, however it can also be done manually at the command line...
- CD into the dir containing the version of .NET that you require eg: C:\WINDOWS\Microsoft.NET\Framework\v1.1.4322
- Run aspnet_regiis.exe specifying the name of the dir you want this set against.
eg aspnet_regiis.exe -s W3SVC/nnn/ROOT/xxx (where nnn is the web site identifier and xxx is the dir name)
eg aspnet_regiis.exe -s W3SVC/1/ROOT/MySampleApp
It's that simple.