Abstract: A method and apparatus for applying focus correction to an E-beam or charged particle system to compensate for wafer warp and mask tilt. In an electron beam system including a registration system which measures the position of four registration marks with the beam and calculates the apparent magnification error of a given chip, means are also provided for using magnification and rotation error information to calculate a height error factor and to apply a compensating current to a dynamic focusing coil of the electron beam to move the effective beam focal plane to a position which matches the wafer or mask plane at each chip site.