We have fabricated YBa2Cu3O7−x–SrTiO3–YBa2Cu3O7−x(YBCO–STO–YBCO) trilayers, in which each layer is patterned photolithographically, capping the first YBCO film with aninsituSTO film. Atomic force microscopy demonstrates that the capping process dramatically improves the quality of the surface of the second layer, allowing the growth of an upper YBCO film with a substantially reduced level of low‐frequency flux noise. A magnetometer with a multiturn flux transformer coupled to a dc superconducting quantum interference device achieved a magnetic field noise of 74 fT Hz−1/2at 1 Hz, improving to 31 fT Hz−1/2at 1 kHz. ©1995 American Institute of Physics.