Duplicate and destroy an EC2 instance in AWS via .NET code

We have an application with long running processes which prevents us from being able to use Elastic Beanstalk to properly scale the environment. In fact no metric scaling would be useful for us and what we really need to be able to do is the following....

• On demand, programatically, create a new EC2 instance which is a duplicate of a specific EC2 "template" instance (That template instance would be an EC2 running IIS with specific code deployed to it, probably via beanstalk).
• On demand, programatically, destroy a specific instance

Based on specific events we would need to perform the above actions via our .NET code base.

I get the feeling that we should be able to do this with cloudformation templates but i dont see any clear documentation to handle this.

Any advise or direction would be greatly appreciated.