If you look carefully to your canvas, you will see that you have 3 Box components. One of them is the one that you don’t need. At this point, you have three options:
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Delete the not needed cube component: just start selecting the box components one by one and when the big cube turns green, that means that that component is creating that cube. Delete it.
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Turn off visibility to the big cube: use the same process described in “1” to detect the big cube component. Them select it and use RMB click over the central area in the component and click on “Preview” option. It will disable the component previsualization but it will keep calculating the cube internally so you can use that data later in your script without having the cube bothering around in your viewport.
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Disable the component: is the same than “2” but selecting “Enabled” instead of “Preview”. This options deactivates the box component calculation. So you won’t have a preview, neither data to play with in your script coming from this component.
I hope this helps a little bit 
Anyway, what you really need is to read properly some of the Grasshopper primers that are all around that explain this things properly.