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extract.exe is a DOS command, you can't just drag files onto it and run it like a Windows application. You must specify the filenames of both ISO tracks, followed by the LBA offset of the second track (as found on the GD-ROM disc) in a command prompt (DOS box).
LBA = logical block address = where a track starts on a disc. When extracting tracks from your GD-ROM disc, write down the LBA number that the ripping software gives you for the second ISO track (not the first).
Then, in a DOS session, type: extract firstdatatrack.iso seconddatatrack.iso 123456 <-- example, of course. The extract command will then write all the files inside the ISO filesystem into your current folder. That's it!
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