The screening of baggage using X-ray scanners is now routine in aviation security with automatic threat detection approaches, based on 3D X-ray computed tomography (CT) images, known as Automatic Threat Recognition (ATR) within the aviation security industry. These current strategies use pre-defined threat material signatures in contrast to adaptability towards new and emerging threat signatures. To address issue, the concept of adaptive automatic threat recognition (AATR) was proposed in previous work by \cite{to7}. In this paper, we present a solution to AATR based on such X-ray CT baggage scan imagery. This aims to address the issues of rapidly evolving threat signatures within the screening requirements. Ideally, the detection algorithms deployed within the security scanners should be readily adaptable to different situations with varying requirements of threat characteristics (e.g., threat material, physical properties of objects). We tackle this issue using a novel adaptive machine learning methodology with our solution consisting of a multi-scale 3D CT image segmentation algorithm, a multi-class support vector machine (SVM) classifier for object material recognition and a strategy to enable the adaptability of our approach. Experiments are conducted on both open and sequestered 3D CT baggage image datasets specifically collected for the AATR study. Our proposed approach performs well on both recognition and adaptation. Overall our approach can achieve the probability of detection around 90\% with a probability of false alarm below 20\%. Our AATR shows the capabilities of adapting to varying types of materials, even the unknown materials which are not available in the training data, adapting to varying required probability of detection and adapting to varying scales of the threat object.