The only time you'd want to clear prefetch would be right after installation during a corporate deployment. Otherwise, clearing prefetch just slows Superfetch and Readyboot down, and will actually make the system slower unless you have an SSD (and in that case, Superfetch and Readyboot are disabled, thus clearing the prefetch data does nothing either way).
What is the reason for the desire to clear the prefetch in the first place? What's the actual issue here, and perhaps we can help with that?