Assuming you can import the file into blender, right click on the model, hit tab to enter edit mode, w, remove doubles. just in case you've got a duplicate shell issue going on making it a wall thickness of 0. additionally, shift+ctrl+alt+m while in edit mode highlights all non-manifold geometry, just hit z to go into wireframe mode first(so you can see it).
As far as manifold. Simply put, Manifold objects are objects that can exist in real life. for example: a plane in 3d modeling is just that, 2D(important note, if you create a new plane in blender and then do nothing it will register as non-manifold!). a box in 3d modeling is visually 6 2d planes that give it volume.. but if you delete one face and leave the others you suddenly have a non-manifold object because it has no volume.
Another example would be if you take a box, and intersect it with another box, its non-manifold because you have faces inside the geometry of another object. some programs can handle this one though, but it is bad design (in my humble opinion). there are a couple other ways you can get non-manifold geometry, do a web search and browse some stackexchange stuff. This is the first site I came across with a quick search
http://3dprintingninja.blogspot.com/2014/07/non-manifolds-your-worst-nightmare.html