A method includes bonding a bottom die to a carrier, and bonding a top die to the bottom die. The top die includes a semiconductor substrate, and the semiconductor substrate has a first thermal conductivity. The method further includes encapsulating the top die in a gap-fill region, bonding a supporting substrate to the top die and the gap-fill region to form a reconstructed wafer, wherein the supporting substrate has a second thermal conductivity higher than the first thermal conductivity, de-bonding the reconstructed wafer from the carrier, and forming electrical connectors on the bottom die.