Every now and then a little gem of usefulness appears on our forum that is just too good to leave it just there. Community member Jeff LaMarche wrote a great tutorial on getting your Blender designs cleaned up and ready to upload to Shapeways. Together with Jeff, I cleaned it up a little and republished it as a full-fledged Shapeways tutorial. Thanks, Jeff!
I've been discovering many of the same things. Another couple of Blender tricks which work really well for cleaning up non-manifold issues:
1) Isolate regions with errors. You may have many regions where there are nonmanifold errors; Jeff's trick about ctrl-+ and shift-h is the baseline here, but don't be afraid to either deselect whole regions of your model before the hide command, or to then select (box select 'b' or circle select 'b,b') whole regions and hide ('h') those for now while you clean up one area before moving on to the next. When you unhide, it'll unhide everything, and so next time you select nonmanifold, you'll have only the remaining sections popping up.
2) Collapse vertices. One of the most common things I see, especially after a Boolean command, is small chains of non-manifold vertices which are either disconnected or connected only at a single point. The trick to getting rid of these is simple. You would do this after cleaning up any obvious, conventional non-manifoldage, such as an un-closed edge; otherwise, that edge will get shrunken to nothing. Basically the criterion for this process is that your nonmanifold regions need to not share an edge between two different "errors."
To clean these up efficiently is easy, once you figure out how. Deselect all, then Ctrl-Alt-Shift-M to select all nonmanifold vertices. Then Alt-M and "Collapse" causes each connected island of selected vertices to collapse to a single point. Now repeat the process - deselect, select nonmanifold, and collapse - once or twice, but be prepared to Undo those commands. Depending on the geometry of the problem, you'll get several possible outcomes. Keep an eye on the number of vertices selected after the collapse command; that's your diagnostic for what types of errors you've just attacked.
- If the problem was a protruding single vertex, or a protruding triangle, this will collapse it down to nothing. As such the subsequent select nonmanifold won't come up with anything; the problem is fixed. You may need to visually inspect for flaws introduced but often there are none.
- If the problem was isolated islands of vertices, this will end with a single vertex continuing to be selected but not made to go away. You can either visually inspect for these (Jeff's Hide Geometry trick is one I figured out for myself when dealing with exactly this), or you can use MeshLab's filter "remove isolated pieces" with a low vertex count to get rid of them automatically. [If there's a Blender equivalent I have yet to find it.]
- If the problem was an open edge or other looped chain of vertices, then the result upon reselection will again by single vertices, but this time they're single vertices with many spokes radiating out from them. Frequently this will have distorted your geometry, and you'll want to undo it and use other tricks (see below).
- If the problem is an open edge that doesn't loop back to itself, then you'll continue to see nontrivial numbers of nonmanifold vertices as you repeat the process; basically you're "peeling back" the edge, but it remains an edge. Undo and attack via other means.
2) Extrude and collapse. This is a trick for "sealing off" all of the open seams on a model simultaneously; very useful for if you, say, decided to lop off a hand so as to replace it with something else. Use this only if you're sure that these are the only kind of nonmanifold errors you've got left, though, as it will produce unuseful or confusing results on other types of error. Deselect all, select nonmanifold, extrude ('e') and immediately hit enter (thus giving zero displacement to the extruded vertices). Then alt-m and collapse to bring all those vertices to the center of their respective chopped openings and clean them up into one vertex. This is much more powerful than using Shift-F to fill the opening, because Shift-F often does strange things near smooth edges or when your contour is a complicated one which doesn't necessarily lie on a plane.
4) Not a Blender trick, but an excellent tool for similar issues: MeshLab's "Uniform Mesh Resampling" filter. If your mesh is badly nonmanifold, such as an attempt at a Boolean union that just won't come out right, then this can be a good alternate tool. Using "Absolute Distance" means that you need not start with a manifold mesh, you'll still get an "outer" and an "inner" surface. Keep both the precision and the offset small, but (in the latter case) nonzero; if you're like me, too small and you get garbage results, but not-quite-too-small can be excellent, and is pretty much always manifold straight out of the gate.