This is another older tutorial that was originally posted on the Shapeways.com forum. 
As the title states, it documents a methodology of handling Non-manifold meshes using the Open Source 3D application called Blender.

Note: this tutorial uses Blender version 2.4x

Document Version: 1.3
Original Publishing: June 17, 2009

Download: Repairing Non-manifold meshes with Blender (2609)