Yes you can note us to cover Vias as a special instruction in your Order.
To have a selection of covered vias, this handling is possible only when you have 2 different sizes of that.
FRor example 0.2mm drills and 0.3mm drills and let us know to cover only 0.2mm. Another way is to have vias placed as a pads, then it is easy to cover vias complete. In this case there we note on the order as well.