For JJ fabrication, either e-beam bilayer resist (organic) mask http://arxiv.org/abs/1105.6204 or inorganic bilayer mask http://arxiv.org/abs/1203.6007v1 could be used. Combination of both could also be used.
Inorganic mask gives potentially better results, but this technique is less developed. After fabrication, JJ-structures, which are planed for electron transport measurements, are not recommended for visualization in SEM, since this results in damage of JJs dielectric AlOx layer.