How do you cube bread?

Only if it's baked in a tin with a rectangular lid, such as for "crustless" loaves. Normal loaves baked in standard loaf tins develop a domed top, making them not cuboid.

"Crustless" loaves are baked in completely sealed cuboid tins, which does mean they develop a cuboid shape. However this may be squashed slightly during packaging.

Clearly, not all bread is baked in a loaf tin - for example French baguettes, bloomers, cottage loaves etc... free-form loaves are never going to be cuboid.