System Engineer Automation and Diagnostics, HE-TEM manufacturing

Work Schedule

Standard (Mon-Fri)

Environmental Conditions

Cleanroom: no hair products, jewelry, makeup, nail polish, perfume, exposed piercings, facial hair etc... allowed, Office

Job Description

Thermo Fisher Scientific Inc. (NYSE: TMO) is the world leader in serving science, with annual revenue of approximately $40 billion. Our Mission is to enable our customers to make the world healthier, cleaner and safer. Whether our customers are accelerating life sciences research, solving sophisticated analytical challenges, increasing efficiency in their laboratories, improving patient health through diagnostics or the development and manufacturer of life-changing therapies, we are here to support them. Our globally distributed team exceeding 100,000 colleagues delivers an unrivaled combination of innovative technologies, purchasing convenience and pharmaceutical services through our industry-leading brands, including Thermo Scientific, Applied Biosystems, Invitrogen, Fisher Scientific, Unity Lab Services, Patheon and PPD. For more information, please visit www.thermofisher.com.

The Materials and Structural Analysis Division (MSD) enables customers to find meaningful answers to questions that accelerate breakthrough discoveries and ultimately change the world. We design, manufacture, and support a broad range of high-performance microscopy and spectroscopy workflows on wafers and single chips that provide images and answers in the micro-, nano-, and picometer scales. We combine hardware and software expertise in electron and ion microscopy with deep application knowledge in the materials science, life sciences, electronics, and natural resources markets. Our worldwide Electron Microscopy colleagues are dedicated to our customers' pursuit of discovery and resolution to global challenges.

How you will make an impact:

As a System Engineer within HE-TEM Manufacturing, you will join the Advanced Manufacturing Engineering (AME) team in Eindhoven. This team works with ground-breaking High-End Transmission Electron Microscopes and aims to continuously improve how these complex systems are built. The AME team analyzes current manufacturing processes and evaluates them in close collaboration with stakeholders across multiple disciplines and departments.

As a System Engineer for Automation & Diagnostics within HE-TEM Manufacturing, you will operate at the critical interface between development and factory operations, ensuring that automation and diagnostic solutions are effectively validated, integrated, and adopted in the manufacturing environment. You will bridge the gap between the Operations Architect's system vision, the Product Owner's delivery roadmap, and the factory execution, ensuring solutions are robust, usable, and deliver measurable impact on cycle time, quality, and efficiency. You will play a key role in testing, validation, troubleshooting, and industrialization of automation solutions, while guiding factory personnel in successful deployment and usage.

What you will do:

• Define and execute system-level validation and verification (V&V) of automation and diagnostic solutions in the factory
• Translate high-level requirements from the Operations Architect into testable system requirements and acceptance criteria
• Collaborate with Product Owner and developers to ensure solutions meet functional and operational needs
• Ensure robustness, reliability, and scalability of automation solutions before release
• Act as the primary interface to factory users and early adopters
• Support deployment and commissioning of automation solutions in production
• Guide factory personnel in usage, troubleshooting, and continuous improvement
• Identify and resolve integration issues in real manufacturing environments (cleanroom, system level)
• Lead root cause analysis of issues in automation and diagnostics
• Drive structural improvements based on factory feedback and performance data
• Work closely with AI/Software engineers to refine models, workflows, and system behavior
• Monitor system performance and define KPIs for success (cycle time, yield, stability)
• Act as the technical bridge between Operations Architect, Product Owner, Development teams, and Factory Operations
• Translate factory feedback into clear requirements and backlog inputs
• Support prioritization by providing impact-driven insights
• Develop and maintain system requirements, interfaces, and architecture views
• Apply system engineering practices (e.g., V-model, requirements management, traceability)
• Ensure alignment between design intent and operational reality

How you will get here:

Experience & Background

• BSc or MSc degree in a technical field such as Engineering or Physics is required, or a combination of engineering education and meaningful work experience that demonstrates required skills
• 5–10 years of experience in System Engineering within a high-tech manufacturing environment
• Experience with complex system integration (hardware + software + processes)
• Proven experience in validation, verification, and troubleshooting at system level
• Experience in automation, diagnostics, or data-driven manufacturing solutions
• Background in electron microscopy or similar high-tech systems is highly preferred

Technical Skills:

• Strong understanding of system engineering methodologies (V-model, requirements engineering)
• Strong understanding of manufacturing processes and system integration
• Strong understanding of validation & verification strategies
• Experience with data-driven or AI-enabled systems (preferred)
• Experience with debugging complex system interactions (HW/SW/process)
• Statistical engineering / Six Sigma (Green Belt preferred)

Soft Skills:

• Strong stakeholder management across technical and operational domains
• Ability to translate between strategy, development, and operations
• Hands-on, pragmatic mindset with strong ownership
• Excellent communication skills (technical & non-technical audiences)
• Comfortable working in a dynamic, cleanroom manufacturing environment

Our offer

• Direct contract with Thermo Fisher Scientific with a competitive salary, 13th month, holiday allowance and annual incentive bonus.
• A flexible working hours arrangement.
• Excellent career progression opportunities within a growing global employer.
• Training and courses are available via our Thermo Fisher University to continuously develop yourself.
• Collaborative work in an international environment.
• Strong Team Spirit and many company and team activities.
• Very attractive 40 holidays a year.
• This is a full-time position (40 hours).
• We welcome candidates that enjoy working in a diverse, multi-disciplinary, groundbreaking technology environment where personal development and team cooperation are key to success, to make the impossible possible for our customers.

Diversity in our teams is an essential element to build an effective and challenging working environment. Integrity, Intensity, Innovation, and Involvement are key values that we expect of all that are part of our community.

Apply now! 

Thermo Fisher Scientific does not discriminate based on race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or any other legally protected status.