Conductive vs Non-Conductive Filled Vias

Conductive Fill

Generally, a conductive filled via will be used when heat or a large amount of current needs to be carried from one side of the board to another. These can be found under chips that will be giving off a lot of heat where overheating is a concern. The metallic nature of the fill will naturally wick heat away from the chip to the other side of the board in many ways like a radiator.
The main drawback to conductive filled vias is the difference in CTE (Coefficient of Thermal Expansion) between the metallic fill and surrounding laminate. Metal will heat and expand much more rapidly than the surrounding laminate and this may cause fractures between the pads and hole wall. Because of this, conductive filled vias are not recommended for Via In Pad processing where the purpose of the fill is the reinforce the stability of the copper pad that is plated over the hole.

Non-Conductive Fill

A common misconception is that a non-conductive fill will either not pass any or only a very weak electrical signal through the via. This is not true. The barrels of the vias will still be plated with copper the same as any other via on the board, the only difference is the empty air in barrel is replaced with the fill material. This is usually done to prevent solder or other contaminants from entering the via or provide structural support for a copper pad covering the open hole in the case of a Via In Pad. Non-Conductive fill is another term for mask plugged vias.