The described embodiments relate generally to electronic devices and more particularly to methods for selectively encapsulating circuit boards and other electronic components contained within electronic devices. A first encapsulation layer can be limited to specific regions of a circuit board using a variety of processes including molding, laser ablation, etching, milling, and the like. Secondary assembly steps can then take place in the regions where the encapsulation layer is removed. In some embodiments, secondary encapsulants having various thermal, electrical, and optical characteristics can fill openings left in the first encapsulation layer to aid in the operation of underlying components.