I got my crankshaft from machining. Polished journals and freshly balanced. But after storage without protection i have some surface rust on those three spots. Can i leave them or should i remove it? If i should remove it which method is the best?

 

Someone else will chime in, but some 000 or 0000 steel wool and some wd40 should clean that up. I would assume.

 

Agreed.
Renove it. Would even step up to the red scotchbrite if needed paired with aforementioned WD40.
Less rubbing is more in the oil seal areas.

 

I polished with my Dremel tool and some high cut compound. Everything is gone. Thank you.

 

I would recommend soaking in vinegar.