Ions are charged atoms. In Vacuum you take a small inlet of gas (only very little), or heat up a small piece of solid until it evaborates, depending on what type of atom you want to use. Then ionize it (e.g. having a white glowing hot piece of wire in the vincinity) then accelerate it. With electrodes and coils (like, e.g. used in old CRT TVs/monitors) you can form have a narrow, focused beam you can move around. This all has to be done in vacuum, because the beams will stop in (dense) air immediately.
This is your "cannon" with which you can very precisely aim and shoot at a target.
Where is this done?
The microscopes used for the very delicate structures in modern microchips are normally electron microscope (not using light but electrons for imaging). They operate in a vacuum which is very handy, because in that vacuum the focused ion beams can operate.
So you have your chip in your electron microscope, and you know that buried below some other structure is a signal hidden from plain view (maybe on purpose on a secure chip, but maybe you are debugging your own design and it just happens that this is where you suspect the answer to why the chip is not operating as required).
So you set your ion-beam to "heavy noble gas, e.g. Xeon" and shoot particles to drill a small hole until you have a trench down to the interesting signal. But that trench is not wide enough to allow your (huge!) probe needle to contact. You you switch to "deposit metal" and, with much less impact velocity for your particles, like with a small brush, you put in a conductive trace from within the trench to some part on the (still intact) silicon-dioxide protective layer on top of the chip. This is where you put your probe needle that can then access the buried signal.
Ions are charged atoms. In Vacuum you take a small inlet of gas (only very little), or heat up a small piece of solid until it evaborates, depending on what type of atom you want to use. Then ionize it (e.g. having a white glowing hot piece of wire in the vincinity) then accelerate it. With electrodes and coils (like, e.g. used in old CRT TVs/monitors) you can form have a narrow, focused beam you can move around. This all has to be done in vacuum, because the beams will stop in (dense) air immediately.
This is your "cannon" with which you can very precisely aim and shoot at a target.
Where is this done?
The microscopes used for the very delicate structures in modern microchips are normally electron microscope (not using light but electrons for imaging). They operate in a vacuum which is very handy, because in that vacuum the focused ion beams can operate.
If you want to buy, ask your dealer for a "Focused Ion Beam Workstation", e.g. http://www.photonics.com/Article.aspx?AID=50359. Have 100k€ - 1M€ to spend. ;-)
What to do?
So you have your chip in your electron microscope, and you know that buried below some other structure is a signal hidden from plain view (maybe on purpose on a secure chip, but maybe you are debugging your own design and it just happens that this is where you suspect the answer to why the chip is not operating as required).
So you set your ion-beam to "heavy noble gas, e.g. Xeon" and shoot particles to drill a small hole until you have a trench down to the interesting signal. But that trench is not wide enough to allow your (huge!) probe needle to contact. You you switch to "deposit metal" and, with much less impact velocity for your particles, like with a small brush, you put in a conductive trace from within the trench to some part on the (still intact) silicon-dioxide protective layer on top of the chip. This is where you put your probe needle that can then access the buried signal.