It is always possible to realign the head by adjusting rotation until the protractor readings are zeroed. However a zero protractor reading does not guarantee accuracy since it is a sight scale without the benefit of vernier readings. Also, these scales can get misaligned or broken or may be missing altogether. This leaves no trusted reference at all. So the video and procedure below shows how to rough align the spindle without benefit of head protractors.

To quickly align a milling head prior to using a test indicator you can use a machinist's square. Notice the closing of the gap between the square and the quill. This tells you that rough alignment has been achieved. The square must be aligned with the quill in relation to the longitudinal and cross directions.