Flattening & Flattening Artifacts

AFM images generally require some post-processing. AFM images are generated by scaling the Z-piezo voltages to yield a height, and that voltage generally has an offset required to extend or retract the Z-piezo so that the probe can interact with the sample. There is often also a tilt to the sample due to mounting or the cleaving of the substrate which is irrelevant to the surface morphology but nevertheless reflected in the AFM image. The offset and tilt prevent a meaningful interpretation of the AFM image. Such an image is shown at top.


One method of post-processing is flattening. In this case a polynomial of order n is fit and subtracted from every trace and retrace. It is called "flattening" because this method of processing tends to flatten or unroll an AFM image. It is also a potential source of artifacts.

The second image shows a series of photo-lithographed Au pads for directed self-assembly. Flattening was applied in image post-processing. Note the dark regions extending in the fast scan direction on either side of the pads. In AFM any features that are consistently and uniformly aligned in the fast direction are suspect. According to the flattened image the substrate near the pads dips down-- but only on the right and left sides of the pads. This is physically implausible and suspect. Any sections, height, bearing or R_a measurements from this image would be erroneous.

To remedy these artifacts stop bands are placed on the pads allowing only the substrate pixels to be used in the flattening. In this final image stop bands are placed over the pads in the middle portion of the image showing a flattened image without baseline distortions.

In general, flattening works best post processing images that don't have high aspect ratio features: e.g. grains on a film surface. In these applications one is interested in the small scale structure, not the large scale morphology. Flattening long wavelength features away is in fact often desirable. In cases like these lithographed pads flattening can still be applied but beware of artifacts and use stop bands accordingly.