Question on how to remove a part of an object

Hello all. I’m attempting to use Blender to model a starship that I’ve designed for a book I’m writing. I’ve made some progress figuring things out, but I’m having trouble figuring out how to do something.

I’d like to hollow out an a specific section of the ship. This particular ship is essentially designed to be launched from a mass driver.

What that means is that there a tunnel shaped like a cylinder running through a fairly complex object. I suppose I could try to model that vertex by vertex, but what I’d like to know is if there’s a more elegant way of doing this? If I overlay a cylinder will it “erase” the vertexes of another object?

If I overlay a cylinder will it “erase” the vertexes of another object?
This is done with a boolean modifier http://wiki.blender.org/index.php/Doc:2.6/Manual/Modifiers/Generate/Booleans

Expect to do some manual cleanup of the resulting mesh. Don’t skimp on this or you could end up with bigger problems later.

Alternatively you can use snapping or project knife to project a circle onto the faces of your object and do the same as the boolean modifier but manually so you have full control of the mesh.

Google, “making a hole in a mesh Blender”.