Re: Is it possible to create/adapt our own GUI to simulation models.
Yes, although it would require a lot of work, you can technically do that with FEATool Multiphysics (but not CFDTool as it doesn't support scripting).
As all FEATool models can be exported and run as standard Matlab m-file scripts, you can also write your own interfaces around it using the Matlab UI controls. The functions available in the public user facing API are listed in the following link
but the easiest/most convenient way to learn is basically to use the "File" > "Save model as M-file script..." menu option and go from there. For example, the user "randress" built a custom GUI for slicing/splitting geometries: