Working on the nanoscopic scale means that not all of your standard computer vision algorithms will work as you wish. There are a lot of challenges you need to face in order to adjust your methods to work in nanoscale. One of our clients had to confront some of these problems, as their solution required the estimation of the contact point of two nanometer-size objects based on an RGB image sequence. Given our experience in applying computer vision methods to unusual problems, we were able to find a suitable solution for the task.