I've experimented a lot on drilling precisely located holes. This is a technique I've developed for myself and it's working for me. Drilled >20 cases already.
1. First make drawing in FPE software to the size of your panel/case. In the drawing use as narrow lines as possible for increased accuracy.
2. Print it with scale set to 100% (A4, A3, A2 or whatever your panel size is). This is very important to ensure that printer/plotter prints precise size according to drawing. Sometimes the printer outcome is different by fraction of mm/inch to what you expect. It will ruin accuracy. Measure the paper drawing with ruler ot caliper. If not perfect, either calibrate the printer or search for another one. It may take time to find a printer/plotter which prints precisely. Also, make sure you use the following settings as on screnshot attached (this is all about FPE software, other software setting may be different). Print in B/W mode, not color so that only one printer cartridge will be engaged for maximum accuracy).
3. Cut the outer shape (=panel shape) of the drawing with Xacto knife guided by metal ruler.
4. Stick it precisely to the panel by using glue (you will remove it later with solvent). Don't apply too thick layer of glue. As thin as possible. Wait for the glue to harden.
5. Now you proceed to drilling itself. Slightly punch reference points to be drilled on paper with carbide scriber. The scriber must protrude the pater and reach the metal to leave mark on it. This is very important to put the scriber exactly in the center of reference point (funny enough, it's harder than you can imagine). That's why I recommend to apply thin layer of glue and use thin paper for printing. Use good lighting and magnifying glass if necessary.
I use this carbide scriber:
http://www.amazon.com/gp/product/B00004T7S1?psc=1&redirect=true&ref_=od_aui_detailpages00
6. Punch paper (and panel underneath it) with automatic center punch. After you mark the center of the hole with carbide scriber (step #5), it's easy to punch it with center punch, it doesn't wander. I use this center punch:
http://www.amazon.com/gp/product/B000HTAH70?psc=1&redirect=true&ref_=oh_aui_detailpage_o02_s00
Try to punch once only. Only if you see that it is offset, make second ot third strike to remedy.
7. Take good screw-driver drill, preferably cordless. Chuck must be good (tricky to find drill with chuck that doesn't stagger on the shaft).
8. Make starting cavity with drill bit for ceramic tile. It has totally different shape from usual drill, but it doesn't wander. I use this one:
http://my-shop.ru/shop/products/1885540.html?partner=6414&gclid=CjwKEAjwkcWrBRDg5u6SuPS11C0SJAChLLAHXLrav1hkXKRHwcnHVHuU2tZX_i9WsiFiGHJPUOUJKxoCu9zw_wcB
Mine has 4 cutting blades. 2 cutting blades (more common) will do the trick as well, I guess.
Just make small cavity with it. Don't try to drill through, of course. Always apply oil at drilling. I use WD40.
The cavity made by ceramic drill bit will ensure that the final drill bit will not wander.
As you can notice, the whole process is about minimizing wandering of the bit.
8. Now you are prepared to drill the final hole. Don't try to use generic drill bit. Instead, use spotting drill. I use this one made by Europa Tool (if talking about 3mm hole, there are different sizes):
http://www.ebay.co.uk/itm/3mm-HSS-Co8-90-DEGREE-NC-SPOTTING-SPOT-DRILL-EUROPA-OSBORN-8214020300-D25-/271833566150?pt=LH_DefaultDomain_3&hash=item3f4a8b0bc6
What's so special about spotting drill? First, it has very short fluted part. It means that it's sturdy and doesn't bend when you press the drill against the material. Believe me, drill bits under size of 5mm with large fluted part do bend when you press it down.
Then, it has no side cutters. It means that it cuts material only with its tip. Side cutters tend to bite the material which make the bit wander sideways.
Use oil at drilling and VERY low RPM (~1 revolution per second). For that screw-driver drill must be used, not usual drill. Screw-driver drill will maintain torque at low RPM.
Spotting drill is not designed to drill trough thick material, but it's good enough to drill through 3-4mm.
And yes, when drill panel up to 1.5mm thick, don't use drill bench. Better by hand (just control it that you hold the drill vertically).
9. You are done. Remove the paper and clean the panel. Deburring may be needed (I use Noga tools).
This method is about drilling small holes (e.g. for screws, standoffs etc). For large holes (e.g. for Neutrik connectors), knock-out punch must be used (that is another story, and there are also some trick to share).