Direct write nanolithographic techniques are powerful techniques to fabricate masters for nano-imprint lithography (NIL). Proton beam writing (PBW) is a relatively new technique which has shown great potential in fabricating three-dimensional (3D) nanostructures in polymer resist material down to the 20 nm level. MeV protons generate secondary electrons and like in many lithographic processes these electrons modify the molecular structure of the resist. The energies of the proton induced secondary electrons are relatively low compared with secondary electrons generated using electron beam writing, therefore proton induced secondary electrons only modify resist material within several nano meters of the proton track. Since protons mainly interact with the substrate electrons the path of the proton beam is very straight, resulting in smooth and well defined resist structures with practically no proximity effects. Further development of current proton beam technology, required to approach sub 10 nm structuring with MeV protons is discussed. To explore the full micro-and nano-fabricating capabilities of PBW it is important to investigate potential new resist materials. In PBW mass production can be achieved through the fabrication of reliable molds and stamps. The compatibility of MeV proton beams for resist materials and post processing steps like electroplating and resist removal are evaluated. The second focus of this paper is PDMS nanofluidic lab on a chip sorting devices using high quality Ni molds. These molds have been prepared via PBW and Ni electroplating, a release layer on a Ni mold allows fine feature replication down to the 300 nm level with high aspect ratios in PDMS.