Software Engineer Applied Math Jobs in Massachusetts

Onto Innovation is a leader in process control, combining global scale with an expanded portfolio of leading-edge technologies that include: 3D metrology spanning the chip from nanometer-scale transistors to micron-level die-interconnects; macro defect inspection of wafers and packages; metal interconnect composition; factory analytics; and lithography for advanced semiconductor packaging. Our breadth of offerings across the entire semiconductor value chain helps our customers solve their most difficult yield, device performance, quality, and reliability issues. Onto Innovation strives to optimize customers' critical path of progress by making them smarter, faster and more efficient.
Job Summary & Responsibilities
We are looking for a Software Engineer to join the Inspection Business Unit (IBU). Whether you are launching your career or bringing years of deep expertise, what matters most is how you think: we need someone who can hold a global, system-level view of a complex inspection platform-optics, mechanics, electronics, and software-and then zoom into any layer to get into the weeds when a problem demands it.
Because AI coding agents can now generate and refactor code effectively, the critical skill we are seeking is the ability to maintain an accurate mental model of a complex system consisting of optics, electrical, and mechanical subsystems, and effectively map customer problems to the right technical solutions.
Key Responsibilities
Responsibilities will be scoped to your experience level; early-career engineers will focus on the foundational items while senior engineers will take on broader ownership and leadership.
Systems Thinking & Problem Decomposition

• Build and continuously refine an accurate mental model of the full Onto inspection platform-optics, motion, electronics, image acquisition, and software stack.
  
• Translate customer problems and application requirements into well-scoped engineering tasks by reasoning across subsystem boundaries.
  
• Agility to zoom from system-level architecture down into any specific areas: databases, algorithm performance, hardware, data flow, GPUs, GUIs, etc.
  
• Participate in New Product Development (NPD) alongside hardware engineers, application engineers, Technical Project Managers, and Program/Product Managers.
  

Algorithms & Software Engineering

• Apply machine learning, image processing, computer vision, mathematics, and optics to develop algorithms integrated into Onto inspection platforms.
  
• Develop or contribute to optical imaging modeling/calibration and/or image segmentation, classification, and detection algorithms.
  
• Write, test, and debug software to ensure high-quality, reliable operation; optimize for performance and scalability.
  
• Perform or lead (based on experience) requirement analysis, detailed software design, production code development, and associated test plans.
  
• Participate in design/code reviews collaborating with systems engineers, software developers, and other technical staff.
  
• Leverage AI coding agents to accelerate implementation, while maintaining ownership of architecture decisions, design integrity, and code quality.
  

Continuous Learning & Collaboration

• Stay current with academic research and industrial practices in machine vision inspection, image processing, machine learning, and AI-assisted engineering.
  
• Document software designs, system-level rationale, development processes, and troubleshooting steps.
  
• Support teammates and, at senior levels, provide technical mentorship-especially in systems thinking.
  
• Contribute to improving the team's development workflows and tooling, including AI-assisted practices.
  

Qualifications

• 0-5 years of experience.
  
• PhD, MS, or Bachelor's degree in Electrical Engineering, Computer Science, Applied Mathematics, Physics, or related field.
  
• Demonstrated ability to reason about systems at multiple levels of abstraction-from high-level architecture down to implementation details.
  
• Strong problem-solving, analytical, and communication skills; able to articulate complex system behavior clearly to both technical and non-technical stakeholders.
  
• Competency (or demonstrable coursework) in at least one numerically focused environment such as Python or MATLAB, including linear algebra, image processing, and/or machine learning libraries
  

Preferred Qualifications

• Experience in semiconductor inspection, machine vision, robotics, or similar highly technical domains where hardware/software co-design is essential.
  
• Track record of diagnosing cross-subsystem issues that span optics, electronics, firmware, and application software.
  
• Experience effectively using AI coding agents (e.g., Copilot, Cursor, Aider, or similar) to accelerate development.
  
• Experience with software development methodologies such as Agile, Scrum, or Kanban.
  
• Experience with version control and CI/CD practices.
  
• Experience debugging complex multi-threaded software environments.
  
• Familiarity with embedded systems, hardware communication protocols, and/or real-time constraints.
  
• Competency (or demonstrable coursework) in at least one compiled or production language used in large-scale software systems, such as C++, C#, or Java.
  

Why Join Onto Innovation?
At Onto Innovation, we believe your work should matter-and so should your well-being. That's why we offer competitive salaries and a comprehensive benefits package designed to support you and your family. From health, dental, and vision coverage to life and disability insurance, PTO, and a 401(k) with employer match, we've got you covered. You'll also enjoy access to our Employee Stock Purchase Program (ESPP), wellness initiatives, and cutting-edge tools-all within a collaborative, inclusive culture where your contributions are valued and recognized.
Compensation & Growth
• Base Salary Range:
$115,200.00 - $172,800.00, offered in good faith and based on experience, location, and qualifications.

• Additional Rewards: Annual bonus opportunities and potential long-term incentives tied to both company and individual success.
  

Empowering Every Voice to Shape the Future:
Onto Innovation is committed to creating a workplace where every qualified candidate has an equal opportunity to succeed. We evaluate applicants based on skills, experience, and potential - without regard to race, color, religion, gender, sexual orientation, national origin, age, disability, veteran status, or any other characteristic protected by law. We believe diversity of thought and background drives innovation and strengthens our team.
Important Note on Export Compliance
For certain positions requiring access to technical data, U.S. export licensing review may be necessary for applicants who are not U.S. Citizens, Permanent Residents, or other protected persons under 8 U.S.C. 1324b(a)(3).