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Buried irregular interfaces and particulate present special challenges in terms of chemical analysis and identification, and are critical issues in the manufacture of electronic materials and devices. Cross sectioning at the right location is often difficult, and, while dual-beam scanning electron microscopy/focused ion beam instruments can often provide excellent visualization of buried defects, matching chemical analysis may be absent or problematic. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) depth profiling, with its ability to acquire spatially resolved depth profiles while collecting an entire mass spectrum at every “voxel,” offers a way to revisit the problem of buried defects. Multivariate analysis of the overwhelming amount of data can reduce the output from essentially a depth profile at every mass to a small set of chemically meaningful factors. Data scaling is an important consideration in the application of these methods, and a comparison of scaling procedures is shown. Examples of ToF-SIMS depth profiles of relatively homogeneous layers, severely inhomogeneous layers, and buried particulate are discussed.