1. For best Autofocus results, visit the first well (the upper-left corner of your selection) using the Plate Viewer (or the Marked Points list - should be the top entry).
2. Use the Autofocus icon 
in the Resolve3D window to find the best focus. When you are satisfied
with the focus, choose Replace Point
from the Point List window to restate the Z position of that point.
3. In the Design/Run Experiment tool, provide a name for the experiment. Resolve3D automatically creates a subdirectory of your current data folder with the name you provide here. All of the scan data for this experiment are placed in that folder.
4. Click the Run 
icon to
start the scan. You can stop the scan at any time by clicking the Stop 
icon. When
you abort the scan in this manner, scan data is lost for all unfinished
wells.
The most effective way of monitoring the scan is using the Plate Viewer.
It updates its current location indicator whenever it moves in X and Y.