Micro-morphology of the rubber compounds, such as polymer compatibility and carbon black distribution, is one of the most important parameters affecting compound performance. Transmission Electron Microscopy (TEM) technique enables us to examine this micro-morphology, but has many difficulties. It requires high skill for sample preparation, high cost and a long time. Atomic Force Microscopy (AFM) technique is a relatively easy way for detecting these images. Through TM-AFM (Tapping Mode Atomic Force Microscopy) technique, two different polymer domains were distinguished in the unfilled rubber blend (natural rubber/ synthetic rubber blend). In order to verify the images, analogue signal (voltage) histograms for those images were analyzed by Gaussian multi-peak analysis method. Filler morphology was also examined in the filled natural rubber and filled rubber blend compounds. Silica and carbon black showed different behavior in the rubber blend. Carbon black lies predominantly in the polybutadiene rubber domain whereas silica exists in the natural rubber domain.