Medical imaging is a vital clinical and research tool that has made significant strides in the last few decades with impressive advances in acquisition technology. However, image analysis and interpretation is still primarily performed manually, and is difficult to automate. In recent years, major advances have been made that allow more automatic image analysis, understanding, and interpretation. In this paper we introduce the 3D medical imaging analysis and visualization platform, MILXView, and present some of its current and potential usage for medical image analysis, understanding and interpretation. The paper describes the design of the plugin architecture of the software application, a general overview of the plugins and the improvements and additions to the latest version of MILXView. As an example the cortical thickness estimation plugin (MILXcte) is described for performing automatic atrophy estimation of brain MRI.