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Vanishing geometry in nano level

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Hi

I'm trying to plant some nano-cylinders on a larger cylindrical base of [um] dimensions. When I plant 3 cylinders on top with 200[nm] radius, everything works just fine. But if I reduce their sizes to 50[nm], only one of the wires remain. If I add another cylinder of same dimensions, the whole structure just vanishes.

I've already played around with the relative tolerance values. Currently, it's 1e-9. But nothing seems to be working. I've narrowed down the problem to 'form union' section under geometry. But I cannot figure out a solution.

Any advice is appreciated.

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