public class WinManager
{
 [DllImport("user32.dll")]
 public static extern IntPtr FindWindow(string className,string windowName);
 [DllImport("user32.dll")]
 public static extern int SendMessage(IntPtr hWnd,uint msg, IntPtr wParam, IntPtr lParam); 
}

public class WindowKiller
{
	private const uint WM_CLOSE = 0x0010;
	public static void CloseWindow(string className,string windowName)
	{
	IntPtr hWnd = WinManager.FindWindow(className,windowName);
          	WinManager.SendMessage(hWnd,WM_CLOSE, IntPtr.Zero, IntPtr.Zero);
	}
		
}

private void btnTest_Click(object sender, System.EventArgs e)
{
   Thread killer = new Thread(new ThreadStart(this.CloseMessageBox));
   killer.Start();
   MessageBox.Show("Try to close me!");
}
private void CloseMessageBox()
{
   Thread.Sleep( 2000 );
   WindowKiller.CloseWindow("#32770",null);
}