A system and method for generating a plurality of scan profiles based on a desired implant pattern and the uniformity of the spot beam is disclosed. The system scans the spot beam and records the number of ions as a function of position. This is referred to as the linear uniformity array. The desired implant pattern and the linear uniformity array are then combined to generate a composite pattern array. This array contemplates the non-uniformity of the scanned beam and allows the system to create scan profiles that compensate for this. The software may be executed on the controller disposed in the implantation system, or may be executed on a different computing device.