|(I wouldn't have a disposable cup OR a straw...
but otherwise this is a fair representation!)
Structural editing starts with The Giant Spreadsheet which helps me to see where things are too long and also where there are gaps. Colour-coding which characters are in each scene shows me that sometimes characters seem to have wandered off, mid-manuscript. Where did they go? They need bringing back into the fold. Or I see that a thread that I thought was well woven in is actually half frayed and sticking out. Or not tied off at the end. Seeing the big picture helps me to make sure that it holds together the way I imagined it would.
At the structural stage of editing, I'm still working in Scrivener. It's helpful to be able to move scenes around easily and pull out particular threads if necessary. Also if I need to write any new scenes (and I almost always do), it's straightforward to add a new one.
After that, it will be a final polish and then off to the publisher. And then when my editor there has had a look, there will be no doubt be more editing, but hopefully not too much.
I seriously have no idea how people manage to write a book every three months!