In IIS 6, I can use the Web Service Extensions folder in Inetmgr to allow/prohibit isapi filters, such as ASP.net. I want to be able to do this programmatically (in particular, from an installer script/exe).

Any ideas?
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Adding Web Service Extension Files Using Iisext.vbs should be pretty much what you’re looking for (the linked article describes how to add a new filter: if you just need to enable it, scroll down and see the list of linked articles for exact instructions on how to achieve that)