To do a MICR alignment you must load your printer with the check paper that you use to print checks on. Press the button. You will be prompted to select a check paper layout that corresponds with the check paper you have loaded.
Next the MICR Align screen will appear. Alignment is specific to the paper tray that the check paper is loaded in. Highlight the paper tray name in the list.
Click the button to do the alignment. Use the clear plastic overlay that came with your software or follow the instructions on the page and use a ruler to measure the alignment. Adjust the alignment using the offsets in the highlighted row.
Repeat the alignment by pressing the button again.
Repeat the above process for each paper tray that you will use to print checks.