Abstract: A method for incorporating an ion implanted channel stop layer under field isolation for a twin-well CMOS process is described in which the layer is placed directly under the completed field isolation by a blanket boron ion implant over the whole wafer. The channel stop implant follows planarization of the field oxide and is thereby essentially at the same depth in both field and active regions. Subsequently implanted p- and n-wells are formed deeper than the channel stop layer, the n-well implant being of a sufficiently higher dose to over compensate the channel stop layer, thereby removing it's effect from the n-well. A portion of the channel stop implant under the field oxide adjacent the p-well provides effective anti-punchthrough protection with only a small increase in junction capacitance. The method is shown for, and is particularly effective in, processes utilizing shallow trench isolation.