3d mesh to a line!

Hi,

I am using a software (amira) wherein I generate a 3d mesh and measure the shortest distance of center of triangle on that mesh to another 3d mesh . So, basically I have the coordinates of the vertices (3 coordinates) of the triangle and the corresponding distances stored. Now iven this info, I would like to do a transformation of the coordinates so that the two first principal components of these data lie on the x-y plane (for a more or less planar surface, I want to align the surface to the x-y plane). Then I could plot things nicely in a 3-D plot, or even look at the average distance in y along the x coordinate.

Can someone please help me in this. I am new to matlab/scripting. Hence any resources will be appreciated. I can provide with the data if necessary.

Thanks!