Despite recent advances in metal oxide thin-film transistor technology, there are no foundry processes available yet for large-scale deployment of metal oxide electronics and photonics, in a similar way as found for silicon based electronics and photonics. One of the biggest challenges of the metal oxide platform is the stability of the fabricated devices. Also, there is wide dispersion on the measured specifications of fabricated TFT, from lot-to-lot and from different research groups. This can be partially explained by the importance of the deposition method and its parameters, which determine thin film microstructure and thus its electrical properties. Furthermore, substrate pretreatment is an important factor, as it may act as a template for material growth. Not so often mentioned, plasma processes can also affect the morphology of deposited films on further deposition steps, such as inducing nanoparticle formation, which strongly impact the conduction mechanism in the channel layer of the TFT. In this study, molybdenum doped indium oxide is sputtered onto ALD deposited HfO2 with or without pattering, and etched by RIE chlorine based processing. Nanoparticle formation is observed when photoresist is removed by oxygen plasma ashing. HfO2 etching in CF4/Ar plasma prior to resist stripping in oxygen plasma promotes the aggregation of nanoparticles into nanosized branched structures. Such nanostructuring is absent when oxygen plasma steps are replaced by chemical wet processing with acetone. Finally, in order to understand the electronic transport effect of the nanoparticles on metal oxide thin film transistors, TFT have been fabricated and electrically characterized.