It is now more than four years since the Federal Circuit's en banc decision in In re Alappat. It is now at least two years since the intertwined events of the Federal Circuit's curious decisions to remand in In re Beauregard and In re Trovato, and the publication by the Patent and Trademark Office (PTO) of its Guidelines on the examination of software-related patent applications. Despite that passage of time, the clarity of the legal status of software-related patents, and particularly those written in article of manufacture format (so-called floppy disk patents), has not improved. Nonetheless, use of such claims in patent applications is said to have become pervasive, in the wake of the PTO's concession to the Federal Circuit in the Beauregard case that computer programs embodied in a tangible medium, such as floppy diskettes, are patentable subject matter . . . and must be examined. . . . As a result, counsel and industrial organizations trying to make business decisions on the basis of advice from counsel are left without a proper basis for making sound predictions as to patentability and potential infringement liability in regard to floppy disk patents. This has lessened security of business expectation in one of the most important areas of technology. This, in turn, is a most undesirable state of affairs, which necessarily affects investment, technological advance, and industrial progress adversely.
Richard H. Stern, An Attempt to Rationalize Floppy Disc Claims, 17 J. Marshall J. Computer & Info. L. 183 (1998)