How can I Remove a Volume from inside another volume?

there is no way to get rid of the pipes?
omg that is what i want , can you explain the circuit , so that i could do it myself? and if possible send me the latest circuit and the baked figure
please do explain the circuit

If you ensure that all the spheres are in contact and they have a way outside the box, then you don’t need the pipes.

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Also, if keeping all the spheres in contact and having at least one intersect the exterior of the box is not an option or not desireable, depending on what the output is for this object (3d printing?) there may be another option: slice up the box into horizontal slices that are thinner than the radius of the smallest sphere, and difference from them.

Then, just don’t union the final slices! 3d print all of them together at the same time.

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Yes. It can be another solution.

1- Create a box.
2- Populate 3d points inside the box.
3- Make spheres from the populated points.
4- Make sure that each sphere has connection to the outside of the box(in order to ensure the succeed of boolean operation)
5- Subtract the spheres from the initial box using boolean difference component.
6- If the output Brep is invalid, convert it into a mesh and bake it.

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You can try the _NonmanifoldMerge Command. But it has a high chance of creating problems down the road.

""The NonmanifoldMerge command creates a non-manifold polysurface from intersecting surfaces and polysurfaces.

This generally only useful for export to analysis programs and can cause normal Rhino operations on these objects to fail.""