Have you tried : Geometry-> Vertex -> Merge...
Not the "Merge Tool".
You may need to run the tool a second time.



Also, if there are any left(There are usually no left-overs if I use LWO format for export):
1 - In polygon mode, with nothing selected: press F two times( I don't know why this works, but it does).
2 - Polygon-> Align.
3 - Sometimes there are still strays left over, in this case you must flip them individually(even if their normal is facing outwards) and apply Polygon -> Align