Abstract: This invention concerns scanning probe microscopes and related instruments (“SPMs”) when used to investigate or measure large samples whose size is a multiple of the typical operational scanning area of an SPM, say 150 ?m×150 ?m at most. To avoid frequent readjustments or other time-consuming human interaction and errors when focusing the SPM, a multi-step, automated method for the SPM-scanning of large samples is disclosed, comprising a “coarse”, i.e. low resolution, non-SPM scanning or mapping step adapted to scan a large sample and providing an integral map of the sample, followed by a preferably mathematical evaluation step identifying areas of interest of the sample, which areas are then subjected to a focused “fine” raster scanning step by the SPM with high resolution. The associated apparatus provides the means to execute this novel three-step process.