In order to process e-mail messages stored into the Apple Mail application you have to save those messages to a plain text file first. Just go through the following steps:
1.- Select the messages you want to extract e-mail addresses of.
2.- Select the File ▸ Save As menu.
3.- Set the format to Raw Message Source and do not include attachments.
4.- Click on the Save button to create the output file.
5.- Launch eMail Extractor and drag and drop the file to it.
6.- The file is processed and e-mail addresses extracted.
The extraction will start right away as soon as you tell eMail Extractor where the results have to be saved. The eMail Extractor window will show you the progress, how many valid addresses have been found, how many duplicates and how many addresses have been discarded.