Recently, visual screening based on CT images become useful tools in the medical fields. However, due to the large number of images and the complexity of the image processing algorithms, image processing technique for the high screening quality is still required. To overcome this problem, some computer aided diagnosis (CAD) algorithms are proposed. Cancer is a leading cause of death both in Japan and worldwide. Detection of cancer region in CT images is the most important task to early detection and early treatment. We have designed and developed a framework combining machine learning based on multi-phase convolutional neural networks (CNN) and temporal subtraction techniques based on non-rigid image registration algorithm. Our main classification method can be built into three main steps; i) preprocessing for image segmentation, ii) image matching for registration, and iii) classification of abnormal regions based on machine learning algorithms. We performed our proposed technique to 25 thoracic MDCT sets and obtained true positive rates of 93.55%, false positive rates of 10.93 /case.