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

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…