A semiconductor device is made by providing a first semiconductor wafer having semiconductor die. A gap is made between the semiconductor die. An insulating material is deposited in the gap. A portion of the insulating material is removed to form a first through hole via (THV). A conductive lining is conformally deposited in the first THV. A solder material is disposed above the conductive lining of the first THV. A second semiconductor wafer having semiconductor die is disposed over the first wafer. A second THV is formed in a gap between the die of the second wafer. A conductive lining is conformally deposited in the second THV. A solder material is disposed above the second THV. The second THV is aligned to the first THV. The solder material is reflowed to form the conductive vias within the gap. The gap is singulated to separate the semiconductor die.