I submitted my paper to a reputed journal two days ago. I got a mail from the editor saying that I need to complete other forms (copyright etc) after he finishes screening. However,I hadn't received my supervisor's approval when I submitted the paper. Now my supervisor has got back to me saying that I should withdraw my paper. Currently the status is "Not Assigned." Do I need to send a withdrawal letter? Or I can wait for the screening result? If I don't pass screen, do I still need to send a withdrawal letter?
Yes, you need to withdraw the paper from formal consideration. This is the only way to stop the process once it's begun. This also actually helps you with later submissions. If the paper is submitted and rejected, then you may have to specify this to other journals that ask about the previous history of the manuscript.
It depends on whether your supervisor is one of the authors/co-authors or not.
If your supervisor is one of the authors of the paper, submitting the paper without all the authors' consent is unethical. You should send the editor a letter to withdraw it.
If you wait until the paper passes the screen process, you are wasting the editor's precious time. If you withdraw it now, he can then proceed to other papers on his desk.
If you are the only author of the paper, I am not sure why you need your supervisor's approval to submit the paper. It would be up to you to withdraw or not.