To create a new UIWindow over the main window

If you are using a window scene try this:

private var overlayWindow: UIWindow!

if let currentWindowScene = UIApplication.shared.connectedScenes.first as?  UIWindowScene {
        overlayWindow = UIWindow(windowScene: currentWindowScene)
    }
overlayWindow.windowLevel = UIWindow.Level.alert
overlayWindow.rootViewController = UIViewController()//your controller or navController
overlayWindow.makeKeyAndVisible()

Xcode 8 + Swift

class ViewController: UIViewController {
    var coveringWindow: UIWindow?
    
    func coverEverything() {
        coveringWindow = UIWindow(frame: (view.window?.frame)!)
        
        if let coveringWindow = coveringWindow {
            coveringWindow.windowLevel = UIWindowLevelAlert + 1
            coveringWindow.isHidden = false
        }
    }
}

According to the documentation, to receive events that do not have a relevant coordinate value, such as keyboard entry, make it key instead of merely ! isHidden:

coveringWindow.makeKeyAndVisible()

You can even control the transparency of its background, for a smoke effect:

coveringWindow.backgroundColor = UIColor(white: 0, alpha: 0.5)

Note that such window needs to handle orientation changes.

UIWindow *window1 = [[UIWindow alloc] initWithFrame:CGRectMake(0, 0, 320, 320)];
window1.backgroundColor = [UIColor redColor];
window1.windowLevel = UIWindowLevelAlert;
[window1 makeKeyAndVisible];

Finally I know why it doesn't work, because window1 is a method var, and it will lost after the method executed. So I declare a new @property for it, as

@property (strong, nonatomic) UIWindow *window2;

and change the code like

UIWindow *window2 = [[UIWindow alloc] initWithFrame:CGRectMake(0, 80, 320, 320)];
window2.backgroundColor = [UIColor redColor];
window2.windowLevel = UIWindowLevelAlert;
self.window2 = window2;
[window2 makeKeyAndVisible];

it works!

Your window1 object is a local variable, when the code runs out of this method, this object does not exist any more. Any UIWindow object we created will be add to the [[UIApplication sharedApplication] windows], but this array only keeps a weak reference to any UIWindow object, so it's up to your own code to keep the window object existing. Why apple implemented it like this, I guess, is [UIApplication sharedApplication] object exists as long as the app runs, doing so to avoid keeping the UIWindow objects which only needs to exist for a while living in the memory "forever".

What's more, your code could run with MRC.