Microsoft describes the FAT file system as "the ubiquitous format used for interchange of media between computers, and, since the advent of inexpensive, removable flash memory, also between digital devices."
The software giant was granted the patent in 1996 and last December announced that the FAT patent and three other related patents were to be included in a new licensing portfolio.
But the newly formed Public Patent Foundation (PubPat), which lobbies against the current patent system, questioned the company's motives, speculating that the fact that the portfolio did not include licenses for use in free and open source software meant that Microsoft intended to use its patents to fight the competitive threat posed by free software.
In April it filed a formal request with the US Patent and Trademark Office to revoke the patent, explaining that this is the oldest of the patents in the FAT File System portfolio and that it was likely that, if held invalid by the Patent Office, each of the other patents will be viewed similarly.
The lobby group submitted evidence of prior art - that the feature being patented was already in the public domain - and it is this that seems to have swayed the USPTO, which has now issued a preliminary rejection of the patent.
"The Patent Office has simply confirmed what we already knew for some time now, Microsoft's FAT patent is bogus," said Dan Ravicher, PUBPAT's Executive Director. "I hope those companies that chose to take a license from Microsoft for the patent negotiated refund clauses so that they can get their money back."
Microsoft now has a chance to respond to the USPTO, which will issue another preliminary ruling before making a final decision. If unfavourable, Microsoft may then appeal to the US Supreme Court.