There are several design methodologies you can start looking at.
I'd seen very good results when you get rid of the design freeze stage early on the development process and use "set design" methodology. This is only cost effective when your prototype costs are low. There are many methodologies that aim to answer this question but it depends on the particular machine/process/part
i am not sure what you mean by machine design. Anyway, you can have a look on our attached paper that can give our way of thinking to design a specific machine for marine renewable energy converter (optimization process that can handle the cost-effectiveness issue).