union overlapping spots

[clankill3r]

hi,

i had heatmaps of a ground scan where each layer is a certain depth in the ground.
I made a small program in java to clean things up. Here is the result

Screen Shot 2013-10-03 at 11.14.29 PM.png

It's for a penplot, but at it's current state it still has to many edges so i want to clean it up.
Let's say i have 2 boxes:

Screen Shot 2013-10-04 at 1.10.07 PM.png

Then box A touches box B. In this case i could do a boolean union. But i was wondering if there is another way? Since i have more objects then i can count...
The reason i want to merge is that i have a plugin for sketchup to get rid of coplanar edges.

To make it even harder, the thing is one mesh.
But i could probably make a script to import coordinates of the boxes with their sizes.

Either way, it's for a exhibition that starts next week so any help is welcome.

[Lord Futzi Voldemort]

Maybe topolizer or polygonzer can do something for you. It may be worth a look. Maybe Eric has an idea:
http://www.mootzoid.com/
I also remember he made a tool once to convert a mesh into vertexes without the faces, maybe you can use that to remesh, but otherwise I've no idea.