Ahh, I finally think I understand.

First off, making meshes from unordered point clouds is a well-studied 
but tricky problem, and it's probably not worth attempting to solve 
yourself unless you really want to spend some time on it.  The best bet 
if you want to go with this approach is to try the software I linked or 
look for other existing packages (google for `point cloud mesh' or 
`point cloud reconstruction' or something like that).

Since you have well ordered meshes for each scan the easiest way to go 
if you're writing your own software is almost certainly to operate on 
the individual scans as meshes and then merge them at the end.  Since 
(as I understand it) the structure of the scans is essentially a wrapped 
rectangular grid, like the intersection of the latitude and longitude 
lines on a globe, the process to simplify a scan mesh is almost 
identical to those used in LOD (level of detail) terrain 
simplifications.  You can google it for more info, but time permitting 
I'll see if I can whip up some example code for you to look at in the 
next few days.

Simplifying the point clouds themselves is relatively simple to do 
(depending on how smart you want to make the simplification process), 
but if you want a mesh at the end it's probably easier just to stick 
with meshes throughout.

On another note, this commercial software looks like it may do what you 
want as well:

http://www.3dreshaper.com/en1/En_software.htm

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