Biomedical flow problems tend to involve domains which are geometrically complex over a range of scales. Much effort has gone into developing tools for generating computational meshes automatically from medical scan data (MRI, CT), allowing the easy creation of patient-specific models of the flow domain, and hence the investigation of flow under existing conditions. One obvious enhancement to this capability is to be able to interactively modify the geometry; this would for example allow the prior determination of the effect of certain surgical procedures. In this paper we report on the application of new techniques allowing the insertion of CAD models into the original scan data. The resulting computer program, ScanCAD, has been applied to three case studies illustrating the range of applications for such a technique.