This paper proposes a novel approach to the characterization of critical dimensions and geometric form error at micro and sub-micrometric scales, suitable for application to micro-fabricated parts and devices. Thin foil laser targets for ion acceleration experiments are selected as the test subject in this instance. The approach is based on acquiring areal maps with a high-precision 3D optical interferometric profilometer and on processing the surface topography data with novel techniques obtained by merging knowledge and algorithms from surface metrology, dimensional metrology and computer vision/image processing for quality inspection. This new approach allows quantitative measurement results for the thin foil laser target to be obtained, and shows promise for being applied to a wide array of similar problems involving quality inspection of micro-parts and devices, and to structured surfaces in general.