AFM Workshop


SEM and AFM Scanning Complementary Images

Researchers and process control facilities are increasingly seeking instrumentation to visualize surface features and to make spatial measurements at the nanoscale. The instruments that can provide nanoscale visualization and measurement fall within the Electron Beam Microscope and the Scanning Probe Microscope groups. The most commonly used Electron Beam Microscope is the Scanning Electron Microscope (SEM), while the most common type of Scanning Probe Microscope is the Atomic Force Microscope (AFM). There are advantages and disadvantages to both the AFM and the SEM.

  • To address imaging surface structures, the scanning electron microscope (SEM) and atomic force microscope (AFM) have complementary capabilities. SEM's have fantastic depth of field, and are capable of imaging structures that have a strong vertical relief. AFM's have poor depth of field, but provide amazing contrast on flat samples. The unique capabilities of the SEM and AFM are demonstrated in such extreme examples as the SEM's ability to image a fly's head, and the AFM's ability to image structures on polished silicon.
  • Images measured with an SEM give a direct representation of surface features, requiring no image processing. AFM images always require image processing before optimal viewing of surface structures. It takes time to learn how to avoid inadvertently adding artifacts to AFM images and other common processing errors.
  • AFMs have an advantage in their ability to operate in vacuum, air, and in liquids. The highest resolution AFM images of atomic structures typically require an ultra high vacuum environment. But in ambient air, AFMs can routinely measure images with sub nanometer resolution. SEMs require a vacuum for optimal operation and do not permit high-quality imaging in either ambient air or in a liquid environment.
  • Beyond measuring sample topography, both SEM and AFM can measure surface properties. SEM's advantage is that it can measure the chemical composition of surface features, while an AFM can measure surface physical properties, such as magnetic fields (MFM), surface potential (SKPM), surface temperature (SThM), friction (SFM), and many other surface physical properties.
  • The SEM gives magnification in two dimensions: x and y. The AFM gives magnification in three dimensions: x,y and z. Users can directly measure the height of a sample feature from an AFM image, while typically the SEM sample must be cross-sectioned to obtain the height of a feature. AFMs also provide different magnifications in the x, y, and the z axis.
  • While SEMs scan a sample surface much faster than an AFM, they are not actually faster to use than an AFM scanning. One must account for the time involved in sample preparation, moving a sample into the SEM vacuum chamber, and the measurement session from start to finish. In the end, the SEM and the AFM require about the same amount of time to produce and measure images. It will generally take a few hours for a trained operator to measure images of an unknown sample on both an AFM and an SEM.
  • Thanks to advances in software automation, the learning curve for measuring images with modest resolution on an SEM and an AFM is not too steep. More important to gaining great images on both the AFM and the SEM is investing the time in learning how to correctly prepare samples for scanning and in how to establish specialized scan parameters. Great images are measured by operators on many types of samples.

Imaging Advantage

High Depth of Field

High Contrast





Chemical Composition

Physical Properties



Vacuum, Air, Liquid

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