Provide a specific data file that contains only the vias holes that are to be filled and use an appropriate file name (e.g., Via Filling). Alternatively, if you are supply a native CAD file (Eagle/KiCAD) it can also be a specific or an already existing layer in the design file.
Manually Identify Vias Holes to be Filled in the Drill Editor
Use the Drill editor to manually select the via holes that are to be filled and identify them as Via Filled.
Filling with Resin
The Via Holes are filled with a special plugging resin.