Dear Juzar.

ff3d uses the marching tetrahedra  algorithm to build surface meshes.

This algorithm uses characteristic functions of primitives (volumes). If a 
volume is null or if it does not contain any point of the background mesh, the 
algorithm fails. You are at least in the first situation since your box 
intersects your cylinders' union on there faces y=0.

Best regards,
Stéphane.

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