Solved by David Heffernan.
In my main window, I added a static window field that refers to my main window.
public static Window main; Public MainWindow() { main = this; }
In the windows I need to hide from the task manager and ALT + TAB, I made my main window its owner:
public HiddenWindow() { this.Owner = MainWindow.main; }
It is really simple, it hides the window from the "tasks" tab in the task manager, and also stops people from ALT + TABing in your program.
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