An imaging system may include an imager integrated circuit with frontside components such as imaging pixels and backside components such as color filters and microlenses. The imager integrated circuit may be mounted to a carrier wafer with alignment marks. Bonding marks on the carrier wafer and the imager integrated circuit may be used to align the carrier wafer accurately to the imager integrated circuit. The alignment marks on the carrier wafer may be read, by fabrication equipment, to align backside components of the imager integrated circuit, such as color filters and microlenses, with backside components of the imager integrated circuit, such as photodiodes.