A first insulating layer is formed on a substrate. An opening is formed in the first insulating layer. A barrier layer is formed on the first insulating layer and conforming to sidewalls of the first insulating layer in the opening, and a conductive layer is formed on the barrier layer. Chemical mechanical polishing is performed to expose the first insulating layer and leave a barrier layer pattern in the opening and a conductive layer pattern on the barrier layer pattern in the opening, wherein a portion of the conductive layer pattern protrudes above an upper surface of the insulating layer and an upper surface of the barrier layer pattern. A second insulating layer is formed on the first insulating layer, the barrier layer pattern and the conductive layer pattern and planarized to expose the conductive layer pattern. A second substrate may be bonded to the exposed conductive layer pattern.