[nitrogen]

Wouldn't the planet's atmosphere and oceans fall into the trench?

[CanSpice]

Yes, which is why you dig the trench deep enough to cover it over again, make it airtight, and pump out all of the atmosphere to make a vacuum torus inside the planet.

[drakeandrews]

There were either walls on either side of the trench, or the planet was a barren rock to begin with.