Based on your reply to competent_tech what you want to do is create the GUI using MonoMac.
MonoMac, a new foundation for building Cocoa applications on OSX using Mono.
MonoMac is the result of years of experimentation in blending .NET with Objective-C and is inspired by the same design principles that we used for MonoTouch.
You can use MonoMac to publish applications to the Mac AppStore, to learn about this see the MonoMacPackager page.
What you are describing as a windows 95 looking window, is winforms which is the native .Net API for building GUI applications. With MonoMac you will be able to build a GUI application that uses your current applications source code and looks and feels just like a normal Mac application.
Again trying to call commands on your application is not an ideal way to go about this.