Fabs often thin wafers and perform backside analysis to get at the transistors without going through metal. [Functional IC Analysis] doesn't look like they thinned and they got pretty decent results.

The “professional” mid range solution. Typically some form of Nd:YAG, either the fundamental or some harmonic. Expect minimum of a few thousand USD for a system, probably many more. Probably the most economical would be to piece together a Mitutoyo microscope. Of course, be careful not to look into your home spun laser while firing without good reason.

The “professional” high end solution used for small processes. Equipment is rather expensive. (how much?)

Microprobes can cut traces by moving back and forth. Professional units use ultrasound.

By masking the chip and then etching (ex: with HF) wires can be removed. Masking compounds range from photoresists to nail polish.

Usually done with a fib. Can be done temporarily with microprobes or possibly on a high process chip very carefully with conductive epoxy.

• Functional IC Analysis: http://nedos.net/host2012.pdf