This STM simulator allows to move verticaly the tip of a tunnel microscope. The measured current results from the tunnel effect of the electrons through the barrier between the tip and the sample. You can observe that the tunnel current is extremely sensitive to the distance between the tip and the sample. This allows to position the tip at a given distance from the sample surface with a great accuracy.
In a microscope, the sample is moved horizontally ("Start" button) while keeping the current constant (your job!). Try it, without looking at the sample, and check that the scan corresponds to the sample profile.
In a real STM microsope, the feedback loop is performed using an electronic device an the sample profile can thus be recorded with an accuracy of a fraction of a nanometer.