I have version 3.2.1 for MacBook Pro.
How can I make my MOV file with transparent background so that I can use it in a movie.
Your options are:
1) to export your project as a PNG sequence with transparent background, or
2) to export a video using a green background and then use a chroma key technique in some video editing software such as adobe premiere to remove the background.
You can probably google search both of those topics to find more threads about the subject.