I was examining the mechanical parts given by some available opens sources. Most of them has only Z-axis manipulator. It's OK when you don't care where you land, for me it's crucial.  So what I've saw used 'Adjustment Screw' to adjust the height of stage compared to the  afm-probe. Plus the price tag was awbout 33$ for each. (and we need three of those). 

So I decided to go on a different path. I am familiar with OpenFlexture project, it's an open source 3D DIY printed microscope. The provide both microscope and moving stage with submicron accuracy. 

It has both the moving tray and a placeholder to put RaspberryPi based microscope. 

We will need this microscope to accurately place the nano probe without bending/breaking it. (Also it has place to hold the LED) what else can I ask? 

Now I have to figure out how to mount RaspberryPi based microscope/camera and I am done. Easy peasy, right?