Good morning/afternoon/evening. There are a couple of ways to go about doing what you want to do. Which way is the path of least resistance will depend on how complex the forms 'SecondGUI' and 'ThirdGUI' are.
If 'SecondGUI' and 'ThirdGUI' are merely pop up figures intended to display axes whose display properties will be manipulated from the 'FirstGUI' then you might just consider programmatically creating 'SecondGUI' 'ThirdGUI' figures and using the handles to those figures (which are returned as part of the call to figure) to manipulate the view of the axes.
You can design 'SecondGUI' and 'ThirdGUI' with GUIDE (<http://www.mathworks.com/discovery/matlab-gui.html)>, obtain the code behind file with the callbacks, and instantiate SecondGUI and ThirdGUI by calling the those code behinds and getting any handles to the controls within SecondGUI and ThirdGUI. Then manipulate the display of any axes in there by obtaining handles to the axes and setting their properties.
The official MATLAB GUI user guide (<http://www.mathworks.com/help/pdf_doc/matlab/buildgui.pdf>) contains all you need to know.