was following this tut for making heightmaps in blender and not getting it to work after some digging I discovered that the method only seem to work if the mesh is modelled in blender is this true or can some thing be done to have blender recognise an import obj mesh as a height field.
p.s I should not that the the object imports duplicate vertices and I tend to delete them could that cause the issue
I’m the author of this tutorial  and I don’t see a reason for it to not work in your case (You can make heightmaps/bumpmaps out of virtually any geoemtry) The most important thing in the tutorial is the material-setting for your mesh.
At what point in the tutorial do you get problems and what exactly do you get as a result? Maybe the problem is something simple
EDIT: I supect maybe you are importing the obj with a texture/material already applied. This could be a problem, but should be easlily solved by going into the material panel ([F5]) and clicking on the ‘X’ (Deletes link to this Datablock) next to the MA:xxxx text before creating the heightfield material. … But then again this assumes you’ve skipped the “ADD NEW” part until now
EDIT2: A screenshot of your model + material-panel could help finding the problem.
 Or at least i’ve created the text+images of the tutorial, the ideas came from somwhere on the web or this forum.
Got your email … now it’s clear what’s ‘wrong’ with your imported meshes … either you rotated them in ObjectMode after import or the importer did that without telling you.
The gradient is applied to the objects local axes (these are the ones defined in the “Map to” panel) and is thus rotated as well (i.e no change of colors relative to the mesh) if you rotate the object instead of the vertices in EditMmode. I’ll add a note to the tutorial on that soon.
In your blend file the fastest way to solve this is a simple [Ctrl]+[A]->Apply scale and rotation
BTW: I suggest you to enable “Draw type” = “Shaded” (icon next to “Object mode”) so you can see the result before rendering.