This paper presents a new process for the fabrication of MEMS-based nanoreactors for in situ atomic-scale imaging of nanoparticles under relevant industrial conditions. The fabrication of the device is completed fully at wafer level in an ISO 5 clean room and it is based on silicon fusion bonding and thin film encapsulation for sealed lateral electrical feedthroughs. The fabrication process considerably improves the performances of previous nanoreactors. The wafer-level assembly allows faster preparation of devices, hydrocarbon contamination is no longer observed and the control of the channel height leads to a better flow reproducibility. The channel is shown to be sufficiently hermetic to work in the vacuum of a transmission electron microscope while a pressure of 100 kPa is maintained inside the nanoreactor. The transparency is demonstrated by the atomic scale imaging of YBCO nanoparticles, with a line spacing resolution of 0.19 nm.