If I understand you correctly, you first had a 1-tier (desktop) app that was saving a file using C# to the user's file system. You are now trying to transition to a 2-tier app with your C# code running on the server tier, and the user's browser representing the other tier. There is nothing you can do in C# on the server to write a file to the browser user's file system directly.
That being said, what you need to do is write the file to the HTTP response stream with a content type of something like application/octet-stream. Are you actually using ASP or ASP.NET? If the latter, you should have access to the response stream through a variety of means, but start with the Response object (available from the page, but also available via HttpContext.Current.Response).