Many of today's advanced materials are prepared using a combination of ultrasonic disk cutting, dimpling, and ion milling. In order to optimize the analytical results from a single specimen, several improvements have been made in instrumentation for ultrasonic disk cutting. Also, a system has been developed for detecting either at or near-electron transparency in TEM specimens. Both of these aspects are described. Examples are provided for silicon, metal/ceramic composites and blanket substrate layers for electronic devices.