You can have a HTTP handler to serve out your PDFs like this:
public void ProcessRequest (HttpContext context) {
// Get your file as byte[]
string filename = "....file name.";
byte[] data = get your PDF file content here;
context.Response.Clear();
context.Response.AddHeader("Pragma", "public");
context.Response.AddHeader("Expires", "0");
context.Response.AddHeader("Content-Type", ContentType);
context.Response.AddHeader("Content-Disposition", string.Format("attachment; filename={0}", filename));
context.Response.AddHeader("Content-Transfer-Encoding", "binary");
context.Response.AddHeader("Content-Length", data.Length.ToString());
context.Response.BinaryWrite(data);
context.Response.End();
}