A system and method for noise compensation of a charged particle beam location includes one or more sensors that are spaced apart from each other for sensing magnetic noises within at least one predefined frequency band thereby to provide magnetic noise measurements with synchronous detection of the location of a charged particle beam. Based on the magnetic noise measurements and on relationships between values of the magnetic noises and particle beam location errors, magnetic noise compensations signals are generated. An object is then scanned by a particle beam in response to a desired particle beam scan pattern and the magnetic noise compensation signals.