An array of color filter elements may be formed over an array of photodiodes in an integrated circuit for an imaging device using a carrier substrate. The carrier substrate may have a planar surface with a release layer. A layer of color filter material may be applied to the release layer. The carrier substrate may then be flipped and the layer of color filter material may be bonded to the integrated circuit. Heat may be applied to activate the release layer and the carrier substrate may be removed at the interface between the release layer and the color filter material. The layer of color filter material may be patterned either before bonding the layer of color filter material or after the carrier substrate is removed. A layer of microlenses may be formed over the array of color filter elements using a carrier substrate.