Systems and methods for reducing the buildup of charge during the investigation of samples using charged particle beams, according to the present disclosure include irradiating a first portion of a sample during a first time period, wherein the irradiating the first portion of the sample causes a gradual accumulation of net charge in the first portion of the sample, generating imaging data based on emissions resultant from irradiating the first portion of the sample, and then irradiating a second portion of a sample holder for a second time period. The methods may further includes iteratively repeating the irradiation of the first portion and the second portion during imaging of the sample region. When more than one region of interest on the sample is to be investigated, the method may also include continuing to image additional portions of the sample by iteratively irradiating a region of interest on the sample and a corresponding portion of the sample holder.