Scanning electron microscopy is perhaps the most important method for investigating and characterizing nanostructures. A well-known challenge in scanning electron microscopy is the investigation of insulating materials. As insulating materials do not provide a path to ground they accumulate charge, evident as image drift and image distortions. In previous work, we have seen that sample charging in arrays of metal nanoparticles on glass substrates leads to a shrinkage effect, resulting in a measurement error in the nanoparticle dimension of up to 15% at 10 kV and a probe current of 80 ± 10 pA. In order to investigate this effect in detail, we have fabricated metal nanostructures on insulating borosilicate glass using electron beam lithography. Electron beam lithography allows us to tailor the design of our metal nanostructures and the area coverage. The measurements are carried out using two commonly available secondary electron detectors in scanning electron microscopes, namely, an InLens- and an Everhart-Thornley detector. We identify and discriminate several contributions to the effect by varying microscope settings, including the size of the aperture, the beam current, the working distance and the acceleration voltage. We image metal nanostructures of various sizes and geometries, investigating the influence of scan-direction of the electron beam and secondary electron detector used for imaging. The relative measurement error, which we measure as high as 20% for some settings, is found to depend on the acceleration voltage and the type of secondary electron detector used for imaging. In particular, the Everhart-Thornley detectors lower sensitivity to SE electrons increase the magnitude of the shrinkage of up to 10% relative to the InLens measurements. Finally, a method for estimating charge balance in insulating samples is presented.