In the Epson Scan window, choose Professional Mode. At the bottom of the window click Configuration... which will open another window. Click the Film Size tab and select 6x6 in the pull down menu, and click OK.
Now go back to the Epson Scan window and select Document Type, Film Type, Image Type, and Resolution. Next, Preview so you can see your images. Now Scan and select your file's destination, name, and type of file, e.g. Jpeg. In 6x6, you can scan two frames at once. Oh yeah, check the Thumbnail button beneath Preview so you can check your images before scanning. In the Preview window, you will get 2 thumbnail images. You can view them larger individually, but when you are ready to scan, you must return to thumbnail view, then go back to the Epson Scan window and click scan.