// Get a file name relative to the current Web app.
string file = Server.MapPath(@"binMyApp.exe");

ProcessStartInfo info = new ProcessStartInfo(file, "args");
// Redirect output so we can read it.
info.RedirectStandardOutput = true;
// To redirect, we must not use shell execute.
info.UseShellExecute = false;

// Create and execute the process.
Process p = Process.Start(info);
p.Start();

// Send whatever was returned through the output to the client.

Response.Write(p.StandardOutput.ReadToEnd());
Note that the ASP.NET worker process needs to have permissions to access the external application. The most simple way to ensure this is to place it under the bin folder.