To clean the data you will need MeshLab, another open source appliation, primarily used for post-processing scan data. Download Meshlab here: http://meshlab.sourceforge.net/ In MeshLab you will be able ...
Once InVesalius has calculated the model, you can adjust the settings to select only the brain. We did this by filtering out everything but fat tissue then adjusting the levels to select as much of the brain as possible.
Don't worry if other parts are selected - these can be removed later.
Once you are happy with your selection, save out as an STL file.