Real-time compensation of mechanical position error in pattern generation or imaging applications

Improved systems, apparatus, and methods for detecting positions of moving stages and accurately compensating position error during operation (in "real time") are provided. For some embodiments, rather than rely on two dimensional position measurements, measurements in at least three dimensions may be taken allowing compensation for pitch and roll and, therefore, more accurate position measurements. Further, by including a measurement of a beam column, compensation for movement of the beam may be performed.