Just some of the ways of gaining circuitry extraction, and special code can be written to preform certain analysis, etc etc...

List of Analysis Tools:

• AES (Auger Electron Spectroscopy)
• AFM (Atomic Force Microscopy)
• Automated Circuit Reconstruction
• Custom-built hardware
• Debuggers
• Disassembler (Software)
• EDAX (Energy Dispersion Analysis of X-rays)
• Electron Energy Loss Spec
• EFTEM (Energy Filtering Transmission Electron Microscopy)
• FIB (Focused Ion Beam)
• FLASH ROM / PROM / EEPROM programmer/reader
• Fourier Transform Infrared Spectroscopy (FTIR)
• Logic Analyzer
• Mass Spectroscopy
• MFM (Magnetic Force Microscopy)
• Microprobe Station
• Network and Bus Analyzers (Ethernet, CAN, USB, PCI, AGP)
• Nuclear Magnetic Resonance
• Oscilloscope
• Profilers
• Raman Spectroscopy (NMR)
• Reactive Ion Etcher (RIE)
• Scanning Capacitance Microscopy (SCM)
• Scanning Electron Microsc
• Scanning Transmission Electron Microscopy (STEM)
• Secondary Ion Mass Spectroscopy (SIMS)
• Simulators
• Soft ICE (kernel debugger
• Soldering Station
• Spectrum Analyzer, Analog
• Spectrum Analyzer, Digital
• Time-Domain Reflectometer (TDR)
• Transmission Electron Microscopy (TEM)
• USPTO Patent Database
• USPTO Published Patent Application Database
• Volt Meters
• Waveform Generator
• X-Ray Microscopy