You might want to look at the WYKO surface profiler.  In the past, we have
used it to obtain a 3-D profile of patterned x-ray resist.  The following
description is from the homepage of the Center for Advanced Microstructures
and Devices CAMD)

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http://www.camd.lsu.edu/cleanroom/anand1/interfer.html
A standard metrology tool for 3D imaging of microstructures and step
analysis, the Wyko is commonly used to measure surface roughness of thin
films and electroplated materials. Optical measurement of vertical steps
can also be made from patterned metallic films or PMMA.

Features:
         VSI modes of operation with applications between 10 nm and 500um
         5, 10, 20 power magnification

Capabilities:
         Automatic step measurements
         Automatic 3D profiles
         10 nm resolution
         Measurements up to hundreds of microns

Applications:
         Thin film surface roughness
         Step height measurements
         3D viewing of steps or surfaces

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Regards

Yohannes M. Desta
Graduate Research Assistant
MicroSystems Engineering Team
LSU Dept. of Mech. Engr.