Your first draft is always likely to be a little bit messy.
The structural edit, or content edit, focuses on the overall story. Even if you're a plotter rather than a pantser, you might find your story running away from you at times. Sometimes the characters take over and develop a life of their own, sometimes a new plot twist suggests itself halfway through, or the story takes off in a completely different direction to the one you planned. This isn't a bad thing, it's quite normal for fiction writers. Even when we're writing essays we can sometimes disappear down an intellectual rabbit hole and emerge somewhere we didn't expect to be.
In the structural edit, you're looking for the following things:
Plot: Does the plot make sense? Even if it turned out differently to what you originally envisaged, the story still needs to make logical sense. Watch out for plot holes. We fall down a plot hole when something doesn't make sense or is impossible to believe. Think of them like black holes of logic that swallow a reader's attention. If a reader is too busy thinking about something that doesn't make sense, they miss the rest of the story. Make it a smooth ride.
Character Development: Similarly, do the characters make sense? Are they guided by their inner motivation, are they fully developed, do their actions and reactions feel authentic?
Continuity: When we're in the midst of writing, it's really easy to forget simple details, even what colour eyes your characters have. It's good to get out a pad of paper or an Excel sheet and make sure you list all of the features of your characters and locations when you first introduce them. Then, make sure you stick to those details throughout. There's nothing more confusing than Jake entering the room with dark-brown eyes and leaving it with a flash of his bright-blue eyes. Details are important. If you've based your story in the real world or around real events, make sure to double-check any facts you've included. Even Shakespeare slipped up when he said that Bohemia had a coastline when it was actually a landlocked region. But he didn't have access to the internet or an encyclopedia - you do.
Pace: Does the story keep moving? The structural edit is the place to get ruthless with the delete button. There is a saying in editing: 'kill your darlings.' You might have a darling phrase, word or metaphor that you love the sound of, but it doesn't quite fit or move the story forward. Sometimes you have to sacrifice what you want to write for what you need to write. Keep the story rolling, ditch the minutia.
In the structural edit, you're forming order from the chaos of your first draft.