Tiny geometrical irregulatities in model imported from Rhino Im migrating an assembly with over 300 parts as .obj to blender to animate it.
Some of the gaps of the rhino geometry get filled with extremly tiny polygons. The resulting surfaces are well connected and dont overlap. The marked gap-filling surface has a width of 0,0001mm:

Yet those surfaces have extreme effects on the shading of the object:

In the left is a high-poly, in the right a low-poly version. The surface from the first image is still selected, but too small to be seen. Even though the whole surface is really smooth you can see strong shadows.

My question is: What do you think is the most effective way of dealing with such exporting artifacts? 
I know there are many different approaches, like other export options, rebuilding the rhino surface, changing the smoothing of the surface, simplifying the surface etc, but Im new to this program and dont know which is the most elegant way.
Its a bit annoying that such small features have such a big impact. Since I have a lot to export, Im expecting to see this problem over and over again.
If geometry is beyond recovery, but the shape of the object remains intact (like in your case), it can sometimes work to regenerate the object using a combination of the Remesh modifier (with as many levels your machine can handle), and then using the Decimate modifier to simplify the resulting mesh.

In more detail:


The Remesh modifier will approximate your geometry by fitting it to a grid of voxels and connecting them to reform the mesh - a technique which will only approximate your geometry, but can get quite close at high resolutions. The key part here is that once "remeshed", your object will have uniform detail everywhere.
The high level of detail on the resulting mesh will then need simplification (as big flat surfaces will have been created out of many polygons instead of just one or two), which can be achieved well using techniques posted in other answers to this question: using Limited dissolve on the mesh in Edit mode, or applying a Decimate modifier (which has a few more options, but can accomplish the same result).


Note that this strategy will require you to reapply materials, remake UV maps, seams, sharp edges, etc. and is thus to be used as a last resort, or as the first step in your workflow if you are going to perform these steps afterwards.