Yes, I printed and used Agisoft markers. I attached two screenshots in my post. On first is the model and position of the markers around it. On second you can see all the scale bars.
Theoretically, once I put the scale bars and click on Update button on top of the reference pane, the model should be properly scaled, right? And after that when I right click on the model and export it to .stl file it should still be properly scaled, right?
I can't find what went wrong here....