Direct write implants are usually made in registration with pre-existing features on the wafer surface. The accuracy of the registration is a critical component of the error budget for a given device, just as it is for optical lithography layers. We present a scheme for creating alignment marks in field oxide on a silicon wafer. These alignment marks can be applied near the beginning of the process, are robust in a silicon processing environment, and can be reused for multiple layers of maskless implantation. We also present our method of measuring overlay accuracy, and data showing that an accuracy of 62 nm one sigma can be achieved by our system.