There have been many unanswered posts putting the question "How do I reformat my PS2 Memory Card?".
After searching several forums, I finally got the answer on Isonews and successfully tried this procedure. You will need Datel Memory Manager Plus. The method does not work with GS2/AR2 v2.
To format your memory card, boot your PS2 with the Datel Memory Manager Plus CD. You will need to move over to the options (left arrow) menu and press all four shoulder buttons (L1, L2, R1, and R2) on your controller. This will prompt you to format your memory card and erase all data on that card.