In recent years, breast cancers have been diagnosed by several imaging modalities. One of these imaging methods is the diffuse optical tomography (DOT) system. In the presented study, in-vitro data were acquired from a breast phantom using the our designed DOT system. Breast phantoms were reconstructed in three dimensions (3D) using Truncated Conjugate Gradient (TCG) reconstruction algorithm. Then, image processing methods were applied to the raw images. Image segmentation technique was used to distinguish between "object" and "backgrounds". Later, 3D Gaussian filtering was applied to smooth the image and reduce noise. Finally, a three dimensional interpolation was applied to the noise free images in order to obtain a more realistic 3D image of the tissue phantoms. Thus, we have modified most popular image processing methods to apply the DOT images. As a result, we obtained user friendly, fast, accurate and user independent images processing methods for the DOT systems.