[Andy]

Ensure you have entered your licence key into AC3D - this allows the use of plugins. Once they are installed, you will see menu Tools->boolean.

This is what you can use to make holes.

You can also make the same object different ways. e.g. revolve a rectangle to make a tube. Make a rectangle, make a hole in it, then extrude to make a cube with a square hole. etc.

Andy