A new technique is proposed for analysis of the microstructure of carbon-black-filled rubbers using atomic force microscopy (AFM) images for data processing. The idea consists of segmenting the continuous relief of an AFM scan into isolated fragments that reflect the filler network in rubber. Two structural states of filler are defined: aggregates (small-sized, branched fragments of the relief) and micropellets (dense, round-shape structures). All the information regarding the geometry and coordinates of fragments is stored in computer memory. Based on observations of the relative position of the fragments within a relief, separate aggregates are assembled into secondary structures—agglomerates. The microstructure of five polymers (SBR or IR) filled with N220 carbon black (10, 30, and 50 phr) was investigated. Two materials were loaded in tensile tests to examine the microstructure of extended samples. A comparative analysis of the following microstructure parameters is presented: character of distribution and dispersion of filler in the matrix, fractal characteristics of aggregates and agglomerates, aggregate size distribution, micropellets mass fraction and sizes, and the variation of orientation of the filler, its sizes, and the distance between the neighboring pairs of aggregates in materials subjected to tension.