A semiconductor wafer has at least one pre-layer on-wafer alignment mark (pre-layer on-wafer AM) on a top surface of the semiconductor wafer. A baseline check (BCHK) is performed to align a current-layer reticle AM on a current-layer reticle with the pre-layer on-wafer AM. By capturing and comparing signals of the current-layer reticle AM and the pre-layer on-wafer AM, a corresponding coordinate of the current-layer reticle to the semiconductor wafer is calibrated. Finally, a lithography process is performed to transfer the layout of the current-layer reticle AM to the top surface of the semiconductor wafer to form a corresponding current-layer on-wafer AM.