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Biomolecular image analysis creates new perspectives for scientific communities such as chemists, biophysicists, and computer scientists. Data processing changes our understanding about the manner in which biosensing devices function. This information can be used for biological and medical applications alike. A key challenge in the field of nanoscience is to gain an understanding of conjugated polyelectrolyte (CPEs) aggregation with respect to biomolecules such as DNA and/or proteins. Polymers such as CPE are water-soluble multicomponent molecules that combine semiconductor and light harvesting properties and they have been successfully used for fluorescence sensing. We have developed a software tool capable of reconstructing topological images in sequential fashion to provide precise statistical data about the aggregations and composition of deposited material. Atomic force microscopy has been used to analyze various processes of polymer-DNA formation. In this paper, we present a new approach to image analysis and processing of atomic force microscopy (AFM) data. The software presented is based on multistage thresholding and mathematical morphology methods and can be used for any other topological images.