Software Patents–Back in Play

We’ll try a new format for the newsletter. The first section is for founders, CTOs, and inventors. The second has more detail for those who would like to travel down (Alice’s) rabbit hole. 

Since the Supreme Court’s Alice v. CLS Bank decision in 2013, software inventors have faced a more skeptical patent environment in the United States. 2025, however, marked the pendulum swinging back in favor of the patentability of software and other applied technologies.

For software companies that paused or abandoned patent filings after Alice, this is a moment worth revisiting and acting on.

1) Congress introduced the bipartisan Patent Eligibility Restoration Act (PERA), a direct pushback against the subject matter mess Alice created. PERA would eliminate all judicial exceptions to subject matter eligibility (including Alice) and set forth a clear test for patentable subject matter that courts, patent practitioners like yours truly, and businesses would welcome. Even before enactment, PERA is already influencing how the patent office frames eligibility—pushing analysis away from opaque judicial tests and towards clearer statutory boundaries.

2) The United States Patent and Trademark Office (USPTO) created a new tool to overcome subject matter eligibility rejections: Subject Matter Eligibility Declarations. A patent applicant, working with their attorney, can submit this declaration in support of their subject-matter-rejected claims.

3) The USPTO issued notice of intent to change its examiner guidelines to follow a recent administrative decision that recognized practical technological improvements, such as advances in computer functionality, data structures, and learning models, as part of the subject matter eligibility inquiry. This emphasis on applicant-friendly administrative decisions is a clear sign that things are changing.

4) In his first month in office, new USPTO director John Squires signaled that he’s skeptical of the Alice line of cases and is willing to help applicants clear the USPTO’s subject matter hurdles.

Taken together, 2025 delivered good news for software applicants with pending or still-in-development applications.

If you have software innovations that were shelved, delayed, or never filed because of subject matter eligibility concerns, this is an ideal time to reassess those decisions.

—The Detailed Rabbit Hole—

Congress introduced the bipartisan Patent Eligibility Restoration Act (PERA).

Since Alice, inventors—especially in software—have had to navigate a patent system where eligibility is unpredictable, subjective, and tilted against protecting software innovation. PERA itself captures the murky state of subject matter eligibility law:

Many judges of the United States Court of Appeals for the Federal Circuit and of various district courts of the United States have explicitly expressed the need for more guidance with respect to the meaning of section 101 of title 35, United States Code, and many patent owners, and persons that engage with patent owners, complain that the interpretation of that section is extremely confusing and difficult to discern and apply with any confidence.

PERA would put the U.S. back on competitive ground with Europe, where predictable software patent protection has long factored into investment decisions, R&D planning, and commercialization strategy.

It explicitly eliminates alljudicial exceptions and creates a simple framework for unpatentable subject matter:

(D) The following inventions shall not be eligible for patent protection:

(i) A mathematical formula that is not part of an invention that is in a category described in subparagraph (B).

(ii) A mental process performed solely in the mind of a human being.

(iii) An unmodified human gene, as that gene exists in the human body.

(iv) An unmodified human gene that is isolated from the human body, but otherwise the same as that gene exists in the human body.

(v) An unmodified natural material, as that material exists in nature.

(vi) A process that is substantially economic, financial, business, social, cultural, or artistic.

In practical terms, this means that most software inventions, so long as they are implemented in technology and not merely economic or mental activity, would no longer face Alice’s unpredictable “abstract idea” morass.

PERA would restore predictability to subject matter analysis by resetting eligibility around clear statutory boundaries rather than abstract judicial tests. If enacted, it could mark a meaningful shift toward a more practical, innovation-friendly framework. We will continue to update you as PERA progresses through Congress.

The USPTO issued two notices (here and here) with new guidance on a new applicant tool called Subject Matter Eligibility Declarations.

The USPTO SMEDs (because we need more abbreviations) are sworn technical explanations of why an invention is more than an abstract idea. They allow applicants to voluntarily submit factual evidence—such as technological improvements or how the application integrates an abstract concept into a practical application. Applicants can use these declarations to rebut subject matter rejections. Examiners must consider the declarations under the preponderance-of-the-evidence standard and the USPTO notices offer best practices for preparing them, so they are focused, objective, and directly tied to the claimed invention.

Taken together, the notices are careful to say they aren’t changing the law, but they do open a further door for applicants to secure more software patents.

These changes reward applications that are drafted with technical specificity and a clear explanation of how the invention improves computing or other technology—an approach that now carries more weight at the USPTO than it did even a few years ago.

The USPTO issued an advance notice of changes to the Manual of Patent Examining Procedure (MPEP) to better align eligibility analysis with recent, applicant-friendly precedential decisions.

In particular, the USPTO emphasized the importance of the Patent Trial and Appeals Board decision in Ex Parte Desjardins—that recognized practical technological improvements, such as advances in computer functionality, data structures, and learning models, as part of the subject matter eligibility inquiry. The revised guidance reminds examiners to evaluate claims as a whole, giving proper weight to any described technological advances rather than treating abstract concepts in isolation, and to distinguish eligibility from other patentability requirements like novelty and nonobviousness, a common complaint in our earlier articles.

Taken together with the notices, the updated MPEP language and related examiner training make eligibility determinations for software and other tech applications more predictable. This moves eligibility analysis closer to engineering reality and farther from the abstract test quicksand—a shift applicants have been seeking for years.

The new United States Patent and Trademark Office Director, John Squires, at his first patent signing, committed to fight the tide of patentable subject matter rejections.

According to IPWatchDog, “In his remarks during the patent signing today, Squires underscored his commitment to granting patents on ‘applied technologies,’ including those that have been ‘too often dismissed as mere business methods or ineligible diagnostic practices.’” Director Squires even referenced the 1840 Supreme Court case regarding Samuel Morse’s telegraph, noting that, “Claim 5 of that patent was upheld by the Supreme Court as patent eligible in light of claim 8 being abstract…It reminds us that applied technologies are foundational and form the backbone of America’s growth.” Squires’ citation to this case in particular kicks administrative dust at the Supreme Court’s 2013 Alice decision.

Congress and the USPTO are leading the charge. While courts may evolve more slowly, stronger prosecution records created under 2025’s guidance will improve leverage in licensing, diligence, and enforcement—regardless of what course the courts follow.