#DEFINE precompile by custom GUI

My project had many #define that enable or disable specific feature. If I compile all program it will not fit in arduino. So user must define what kind of hardware have on system and then send firmware to arduino. I want not user to manipulate software so I want to do that by a gui and a graphical step-by-step selections. So user select hardware and all options and gui enable or disable that defines, preprocess, compile and send. It is possible using some kind of software to obtain that?