Not necessary. If you're handing it in person to your superior, usually there's no need for an envelope. Just fold it nicely.
Personally I only use envelope when I'm putting it on my superior's table (in his/ her absence).

What about your HR? In KL or Singapore.

Due to distance, you dont have much choice. Courier or mailing the hard copy is a bit... you know. So my suggestion to email him the PDF copy of your resignation. If yr HR is based in KL, submit a hard copy to them. Otherwise email yr resignation to boss and cc HR inside.