Separating JavaScript in cshtml razor views

I'm new to ASP.NET/MVC3 and I'm trying to figure out how to separate my JavaScript (which contains C#) from the rest of the HTML.

If I put them into .JS files and insert them with a script tag then the C# aspect of them stops working. What is the best way of separating your JavaScript code that also contains C# code in MVC 3 razor?

Thanks.