Python is really amazing language you can build complex software in few lines of code. 

I made very simple/hacky GUI, it has the minimum required to get 2D data. 

It has few stages, connecting to serial port. Calibration of cantilever frequency. Micropositioner control, nanopositioner control and 2D heatmap graph to show output.

It took me more  time than I've expected to connect GUI to firmware but it works now. 

I have only CD-RW as a sample. If someone knows other nano scale structure that I can put under AFM, let me know. ( And it should not cost fortune...)  

Fixed the GUI issues I had now it's working (although with some bugs) as expected