You will need to store a reference to the secondary app in your main app. This will allow you to close it in the CloseRequestFcn of the main app. You can set this function in the main app by selecting UIFigure in the component browser in the design view. See attached picture.
Then assuming you have stored the handle to the secondary app in the main app you can do as follows in the Main App UIFigureCloseRequestFcn
function functionThatOpensSecondaryApp(app)
app.SecondaryApp = SecondaryApp(..);
end
function UIFigureCloseRequest(app, event)
delete(app.SecondaryApp);
delete(app);
end
More details can be found at the link below.
