Abstract: A high-resolution high-throughput ion beam lithography process and apparatus for exposing a large area target by a step-and-repeat process which accommodates lateral wafer distortions in the target and optimizes the resolution, throughput, yield, and cost of the process. First there is provided: a target having predetermined segments defined thereon, with the area of each segment being chosen to optimize the resolution, throughput, yield, and cost of the process; a mask placed in proximity to said target, to define the patterned ion beam; a collimated ion beam with a diameter approximately equal to the diameter of the mask, which is projected through the mask to form the patterned ion beam; and a means for aligning the mask and a selected segment of the target. The size of the mask is equal to or larger than the size of one of the predetermined segments of the target and the pattern area of the mask is smaller than the area of one of the selected segments of the target.