Everything You Should Know About Scanning Electron Microscopy (SEM) — Before Sending Us Your Samples

Posted by Marketing Team on Jul 22, 2025

In the age of evolving materials and miniaturized technologies, the capability to visualize and interpret materials at the micro and nanoscale is no longer a luxury anymore---it is a necessity. Scanning Electron Microscopy (SEM) makes this possible, enabling researchers and engineers to analyze surface features, structures, and compositions with nanometer precision.

SEM can give you the knowledge that light microscopy cannot when it comes to studying next-gen batteries, material failure, or optimizing nanostructured coatings, just to name a few applications. At MSE Supplies, we can provide SEM analytical services to allow you to discover the secrets of your materials - fast, precise and cost-effective.

This guide will cover everything you should be aware of about SEM prior to sending your samples, including how it functions, how it is best used, how samples are prepared, and the equipment that enables the analytical process.

What is Scanning Electron Microscopy (SEM)?

The name says it all—Scanning Electron Microscopy is about scanning. SEM utilizes a highly focused electron beam to scan the surface of an object on a pixel-by-pixel basis, gathering incredibly detailed information about the topography and analysis of a material. However, unlike optical microscopes that depend on visible light and lenses, SEM allows the researcher to view details down to the nanometer scale, as the sample is probed by electrons rather than photons.

At its core, SEM provides a digital, grayscale image that represents how the surface of a sample interacts with the electron beam. Behind such a picture, however, lies a very strong mechanism: the scan is performed through a systematic process that moves the beam across the area of interest in the specimen, with detectors sensing the signals created when the beam interacts with atoms on or near the specimen surface.

What makes SEM so invaluable is its ability to offer exceptionally high resolution and a deep field of view, revealing intricate details of microstructures that are invisible to the naked eye or even to advanced optical microscopes. When combined with other detectors, SEM does not simply take images; it can also provide a window into material composition, grain structure, surface features, and points of failure.

How SEM Works: The Core Principle

An SEM operates by generating a focused beam of electrons from an electron gun at the top of the column. This beam is accelerated through a high-voltage field, concentrated by the condenser and objective lenses, and steered across the sample surface using scanning coils. As the electrons hit the sample, they interact with atoms in various ways, producing secondary electrons (SE) and backscattered electrons (BSE)—the two main signals used for imaging.

The electron beam doesn’t just sit still—it actively scans across the sample surface in a grid-like pattern. Signals are picked up and converted into pixels within a monitor at each scanned point, and the complete picture is created at the end. The resolution of the image sets is a measure of the narrowness and stability of the beam, as well as how effectively the signals from the interactions are detected.

Magnification in SEM

Contrary to conventional microscopes, which rely on optical magnification, SEM magnification is dependent on the level of the sample the beam explores within one frame. The smaller the scanned area is, the greater the magnification. This implies that SEM can zoom into various objects with ranges of 10x to more than a million.

Key Operating Parameters

Accelerating Voltage (kV): This defines the energy of the electron beam. Higher voltages penetrate deeper into the sample and are ideal for denser materials, while lower voltages produce better surface detail with minimal beam damage.

Working Distance (WD): This refers to the distance between the sample surface and the final lens. A shorter working distance generally results in higher resolution and better imaging, but it must be balanced with sample height and detector configuration.

Spot Size: A smaller spot size creates sharper images but with lower signal intensity. Larger spots improve signal but may reduce image clarity.

Vacuum Level: Most SEMs require a high vacuum to prevent the electrons from scattering in air, although variable pressure or environmental SEMs can analyze hydrated or non-conductive samples without coating.

Attachments further enhance SEM's versatility:

Cryo-stages allow the imaging of frozen, hydrated biological specimens.

Heating or tensile stages enable in-situ analysis of materials under stress, temperature, or deformation.

In-situ holders facilitate real-time observation of dynamic material behavior.

What SEM is Best For

SEM excels at providing a detailed visual and compositional understanding of materials at micro and nanoscale. It is especially effective for:

Morphology and Topography: SEM reveals the fine surface structure of materials, whether smooth, fractured, porous, or layered. It captures detail that optical microscopes simply can’t, making it ideal for quality control and structural studies.

Particle Size and Shape: Whether you're analyzing powders, crystals, or debris, SEM can measure and characterize the distribution and shape of particles accurately and consistently across a population.

Fracture and Failure Analysis: SEM helps pinpoint origins of cracks, voids, and other failure mechanisms, offering clues about environmental exposure, fatigue, or manufacturing defects.

Surface Coatings and Interfaces: With cross-sectional imaging and BSE contrast, SEM identifies coating uniformity, thickness, and bonding issues at interfaces in layered materials.

Contamination Detection: Microscopic residues and foreign inclusions can be imaged and identified, which is vital in semiconductor, biomedical, and aerospace industries.

Elemental Composition and Mapping: When paired with EDS, SEM enables rapid elemental analysis and visualization of elemental distribution across a material surface.

Crystallographic Information: EBSD-equipped SEMs provide data on grain size, orientation, and phase boundaries, essential in metallurgy and advanced ceramics.

Real-World Examples of SEM Analysis

1. Surface Contamination in Ultrasonic Aluminum Bonding

In one case, a customer experienced a failure in ultrasonic aluminum wedge bonding, specifically poor bonding of silver pads. The possible source of contamination was suspected to be the surface. A closer examination of the bonding interface was conducted using SEM-EDS. SEM was used to reveal image irregularities and micro-debris at the surface, and EDS mapping showed the presence of insufficient elements in sensitive bonding areas. This insight helped the customer identify the cause of contamination, allowing them to clean and process more effectively.

2. Calcium Phosphate Precipitation on Biochar

In another example, SEM was applied to the biochar that had been loaded with Ca after the column process. The aim was to monitor the morphology of calcium phosphate precipitates grown on the biochar surface and verify phosphate capture through surface precipitation. The SEM-EDS mapping results revealed the co-localization of calcium and phosphorus, supporting the precipitation hypothesis. This gave the customer the visual and elemental reason that their material and treatment process was working effectively.

Sample Preparation Essentials

Proper sample preparation is crucial to ensure meaningful and high-quality SEM imaging. Across industry, standard preparation methods are used to optimize electron interaction and signal detection.

Conductivity: Non-conductive samples are often sputter-coated to prevent charging. Platinum is commonly used due to its fine grain size, but gold and carbon are also applied depending on analytical needs.

Mounting: Samples are typically secured on specimen mounts using carbon tape for general applications, or carbon paste when stronger adhesion is needed, especially for larger or denser samples.

Drying: Complete dryness is critical. Biological or hydrated specimens must be dried thoroughly—using ovens, vacuum desiccators, or critical point dryers—to avoid vacuum instability and sample deformation.

Size Considerations: Sample height is carefully controlled to match the SEM’s working distance. Most sample holders accommodate pieces with an area less than 51 mm in diameter, while an ideal sample height is typically under 5 mm to maintain proper working distance and avoid interference with internal components.

Biological Sample Prep: Preparation varies by sample type. Fixation, dehydration, and coating are often necessary, and analysts should be consulted to determine the most appropriate method for the material in question.

Supporting Equipment You Might Also Need

Several instruments and tools support SEM operations, enhancing both sample preparation and imaging quality. These auxiliary devices are commonly used alongside SEM systems:

Coating Equipment: Used to deposit a thin conductive layer—often platinum, gold, or carbon—on non-conductive specimens. This prevents surface charging under the electron beam, thereby improving imaging contrast.

Focused Ion Beam (FIB) Systems: Employed to mill, cut, or cross-section samples with nanometer precision. FIB systems are particularly valuable in failure analysis, 3D reconstructions, and preparing TEM lamellae.

Ultrasonic Cleaners: Utilized to remove microscopic particles or contaminants from delicate samples. This step ensures a cleaner imaging field and reduces unwanted signal noise.

Dessicator Cabinets and Laboratory Drying Ovens: Essential for removing residual moisture from biological or porous materials. Proper drying prevents vacuum system failure and ensures stable sample conditions during imaging.

Gloveboxes and Inert Transfer Chambers: Required when working with air-sensitive or reactive samples. These systems enable safe specimen handling and transfer into the SEM chamber, thereby preventing exposure to ambient conditions.

These tools help ensure samples are clean, dry, properly coated, and structurally intact—minimizing imaging issues and maximizing data quality.

Final Thoughts: Maximizing Your SEM Experience

Before sending your samples for SEM analysis, take a moment to consider your goals, the condition of your material, and the insights you hope to gain. Scanning Electron Microscopy is an incredibly powerful technique, but it works best when both the client and the analyst are aligned on expectations and requirements. Knowing the mechanism of SEM, its capabilities, and how to treat the samples gives you a significant advantage.

This guide was created to help you navigate that process confidently—whether you're troubleshooting a failure, characterizing new material, or exploring nanoscale features for the first time. A well-thought-out submission will always bring forth improved, actionable outcomes.

Are you prepared to unlock the full potential of your materials? Make MSE Supplies your solutions provider for high-end microscopy and analysis. Contact our team now to schedule an appointment or request a personalized quote tailored to your SEM project. Check what other Analytical Services are available to you: component content analysis, structural composition analysis, microstructure and morphology analysis and more are all integrated to assist with your R&D, QA, production needs and more.

In the case that you are working on your own samples in your laboratory, we also provide an expansive assortment of preparation tools and equipment like coating equipment, laboratory drying ovens, and general lab products that will help you handle the samples, beginning to end. Think of MSE Supplies as your complete resource for materials science—combining expert analysis, high-quality lab equipment, and responsive support under one roof.

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