The aim of the study was the microscopic evaluation of internal structure of cuprophane and polysulfone membrane and their surface analysis before and after reprocessing. The investigations were performed using an optical measurement system (Digital Instruments), a scanning electron microscope (SEM) and an atomic force microscope (AFM). We confirmed by SEM that reprocessing completely removed biofilm from both membranes surface. The analysis based on AFM visualized channels in the examined membrane. The diameter of the channels varied from 150 nm for cuprophane to 380 nm for polysulfone. The roughness expressed as root mean square (RMS) was higher for cuprophane than for polysulfone membrane. The physical differences between nanostrucure of the examined membranes might be responsible for lower biocompatibility of cuprophane.