Accurate topography measurements of engineered surfaces over a wide range of spatial frequencies are required in many applications. The instrument transfer function (ITF) of the microscope used to characterize the surface topography must be taken into consideration to ensure that the height, or depth, of features with higher spatial frequency content is not underestimated. This applies especially when comparing surface topography measurements made by different types of microscopes. We discuss ITF measurements of a confocal microscope and an interferometric microscope using a binary pseudo-random array (BPRA) standard. BPRA standards are surfaces designed to have constant inherent power spectral density (PSD) over the spatial frequency passband of a microscope. The ITF of a microscope can thus be derived from a PSD measurement of a BPRA standard in a straight-forward manner. We further show how BPRA standards can be used as efficient diagnostic tools to characterize aspects of the imaging performance of topography-measuring microscopes.