An improved method for forming a self-aligned twin well structure for use in a CMOS semiconductor device including providing a substrate for forming a twin well structure therein; forming an implant masking layer over the substrate to include a process surface said masking layer patterned to expose a first portion of the process surface for implanting ions; subjecting the first portion of the process surface to a first ion implantation process to form a first doped region included in the substrate; forming an implant blocking layer including a material that is selectively etchable to the implant masking layer over the first portion of the process surface; removing the implant masking layer to expose a second portion of the process surface; and, subjecting the second portion of the process surface to a second ion implantation process to form a second doped region disposed adjacent to the first doped region.