In evaluating the impact of Alice v. CLS Bank it is important to recognize that "all software is not created equal."
1. In both Alice and Bilski, the US Supreme Court held business methods are not categorically excluded and patent ineligibility arose from improperly claiming an "abstract idea." Yet lower courts are interpreting Alice as nearly always preventing patent eligibility of business methods. Thus, you may get a business method patent in the USPTO, but expect both issuance and enforcement to be a challenge.
2. Non-business method software patents are still issuing in great numbers. In Patent Reform: Impact of Alice on Business Method Professor Dennis Crouch observes a chart in James Bessen's article that indicates a slow-down in issuance of business methods, but no decline in other software categories.
3. Software invention claimed properly in conjunction with a physical process are not likely to held an abstract idea under Alice v. CLS Bank. For example, Diamond v. Diehr held a method for curing synthetic rubber including steps using a mathematical formula and a programmed digital computer was patentable subject matter under 35 U.S.C. §101.
4. US patent claims like those in Diamond v. Diehr will issue may play a role in 3D printing technology because a great patent portfolio define the industry leadership.
Here's some commentary on what other attorney's think:
In 3-D Printing: Challenges and Opportunities (Part I), Michael Rosen describes how 3-D printer technology likely relates to IP and patents in the US.
In Many 3D Printing Patents Are Expiring Soon: Here’s A Round Up & Overview of Them, John Hornick and Dan Rowland discuss key 3D printing patents that are expiring and the recently settled 3D Systems v. Form Factor case.
In Formlabs, 3D Systems settle their 3D printing patent battle, Signe Brewster notes the 3D Systems v. Form Factor settlement after two years of litigation, but cautions that startups should not draw too much comfort given the patenting efforts in this industry.
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