The study of polished cross sections is a well-assessed and practical method to investigate the stratigraphy of paintings and multilayer polychromies on works of art, in general. Analyses on cross sections allow us to characterize, at once, all the layers in the stratigraphy, giving information about the artists technique, the number of layers and their composition and sometimes about the conservation history of the artefact. In this paper, the application of an imaging detector focal plane array (FPA) coupled to an infrared (IR) microscope has been studied, focusing on the characteristics and potential of the different working methodologies (attenuated total reflectance (ATR) and total reflection). FPA detector coupled with ATR crystal can "localize" IR information coming from a 30 × 30 μm sample area, in a 64 × 64 dot matrix detector. In particular, an innovative analysis methodology has been tested for the total reflectance measurements in order to obtain maximum information with single measurements. Micro-infrared total reflection measurements have been carried out in an extended IR range (from 1,000 to 5,266 cm(-1)) exploiting the broad spectral response of mercury cadmium telluride detector in order to include overtones and combination bands from near-infrared spectral range without any modification of the standard mid-infrared micro-FT instrumentation. The potentialities of this new approach have been successfully transferred in the imaging/mapping investigations with a minimal tuning of the apparatus. Results obtained on a polished cross section coming from a modern painting and on a micro-sample of a wood polychromy from an undated historic polyptic are shown for demonstration.