The goal of radiotherapy is to eradicate tumors while sparing healthy tissues from radiation damage. Therefore, accurate definition of tumor and organ boundaries is important for achieving good treatment outcome. Organ segmentation is a standard procedure done in radiation therapy treatment planning. Computed tomography (CT) images are commonly used for this purpose. In this paper, we present the development of CTScanTool, the semi-automated organ segmentation tool developed in MATLAB with the graphical user interface. The segmentation method is combined between region growing, morphological reconstruction and watershed transform algorithms. The semi-automated segmentation results of CT images were compared with those contoured by an experienced radiation oncologist. In the experiment, we investigated the combined segmentation method on brain, lung and kidney tissues. In all cases, the agreement was better than 90% for the dice coefficient and the true positive rate-based evaluation. In the near future, CTScanTool will be incorporated in the Proton pencil beam Scanning treatment PLANning system (PSPLAN), which can be used for research and education in proton therapy.