Today, ultramicrotome cutting is a practical tool, which is frequently applied in the preparation of thin polymeric films. One of the advantages of such a technique is the decrease in surface roughness, which enables an effective recording of further morphological changes of polymeric surfaces during their processing. In view of this, we report on ultramicrotome-cut polymers (PET, PEEK) modified by a KrF excimer laser with simultaneous decoration by AgNPs. The samples were immersed into AgNP colloid, in which they were exposed to polarized laser light. As a result, both polymers changed their surface morphology while simultaneously being decorated with AgNPs. KrF laser irradiation of the samples resulted in the formation of ripple-like structures on the surface of PET and worm-like ones in the case of PEEK. Both polymers were homogeneously covered by AgNPs. The selected area of the samples was then irradiated by a violet semiconductor laser from the confocal laser scanning microscope with direct control of the irradiated area. Various techniques, such as AFM, FEGSEM, and CLSM were used to visualize the irradiated area. After irradiation, the reverse pyramid was formed for both types of polymers. PET samples exhibited thicker transparent reverse pyramids, whereas PEEK samples showed thinner brownish ones. We believe that his technique can be effectively used for direct polymer writing or the preparation of stimuli-responsive nanoporous membranes.