The JWNC has 750 m2 of zoned cleanroom space designed to allow interdisciplinary nanofabrication activities to proceed efficiently and with minimum cross contamination of processes. The cleanroom suite has 15 rooms on two levels with lithography tools and scanning electron microscopy facilities at ground level. The column room for the VB6 UHR EWF lithography tool is class 10 , four rooms are class 10,000 and the remainder are class 1000. Each room has an assigned activity such as photolithography or metallization. On the upper level there are 32 laminar air flow cabinets each dedicated to specific tasks, for example substrate cleaning. There are strict controls on the movement and washing of all glassware in order to minimise cross contamination.

A building management system linked to numerous control valves and sensors automatically monitors and controls room temperature and humidity levels to optimise equipment performance and maintain stable processing conditions within the JWNC. For instance, the column room temperature for the VB6 UHR EWF lithography tool is continually maintained at ±0.1 °C. Bulk liquid nitrogen tanks outside the JWNC provide a liquid nitrogen feed and a supply of high purity nitrogen gas. Numerous gas specific sensors located throughout the centre are linked to a central gas detection and alarm system - an important safety feature given the comprehensive dry etch and deposition facilities within the Centre. Prior to constructing the JWNC extensive vibration surveys were carried out and this information was used to design the large concrete plinth which forms the base of the VB6 UHR EWF lithography tool. To minimise disruption and possible equipment damage arising from power failure, the VB6 UHR EWF lithography tool has a UPS which maintains the tool plus essential compressed air and chilled water supplies for up to 30 minutes. A backup diesel generator simultaneously starts a few moments after power failure.