Systems and methods generate a modified application data structure that provides a customized modeling of physical systems in response to customized user inputs received via application feature(s) for new window form(s). The modified application data structure is generated from guided user inputs received through application builder wizard graphical user interface(s). The systems and methods include embedding a multiphysics model data structure in an initial application data structure and defining new window form(s). Window form data representing the defined new window forms is added to the initial application data structure. User-selectable application feature options are displayed in the application builder wizard graphical user interface(s) and application feature data is added to the initial application data structure to create a modified application data structure. The added application features can include data representing widget(s), form feature(s), and command sequence(s).