I created a website project where I set the ASP.Net version on the website to 2.0.50727. I noticed that on install an aspnetclient dir gets created on my file system within the project dir. When I uninstall the project, the aspnetclient dir gets orphaned rpeventing the project dir from being removed on uninstall.
You could use a custom action to remove the files/folders that were added by ASP.NET registration. If you sequence the action before RemoveFiles, that should allow the installation folder to be removed.
