For doing one off cases at work i use a proper drill press and good drills in the right size. After drilling comes filing. You need some good but small files for metalwork. Larger Breakouts are drilled first, then roughly cut to shape with a dremel and the rest is - filing.
Holes for Buttons and stuff that you have the right drill bit for: - Mark exactly where to place it (I always prefer a scriber for all markings related to mechanical work).
- Hit the center with a center punch to give the drill bit some guidance. This way it won't wander around on the surface.
- Use some clamping if you work with metal or small parts, don't wear gloves when working with rotating tools (danger of getting sucked in). For larger Plastic parts and very small drill sizes this can be skipped, but I do not recommend that! Clamping is not only for safety: it makes sure your drill goes down exactly where you want it because the workpiece cannot wander away. Of course it takes more time to align the piece exactly and clamp it down at that very position precisely. But it is worth your time if you care for the looks! Larger drills need smaller speeds, little drills are allowed to turn faster. (10mm about 600 to 800 RPM, 4mm about 1200 RPM as rule of thump). It takes some practice, but you will hear and feel if the speed or pressure is wrong: The drill starts to rattle, it sounds wrong, the material behaves somehow unexpected - you get it with practice. Too slow turning drills won't do good, too: They tend to get caught and then can possibly break or give a bad looking hole.
- deburr with a countersink (I prefer a handheld one, but it can be done with the drillpress in the same clamping position. Danger with doing so is to leave a very deep groove as I find it hard to get the height right. By hand you have better control.
Larger Holes for Buttons and stuff bigger than your maximum drill bit size: This happens often with connectors and stuff. Most simple drill presses can only take drill bits up to 10 or 12mm in diameter. You need a hole cutter

for that. I would only recommend them for plastics and possibly aluminium, but never for steel! For steel and also aluminium I prefer these screw piercers:

The rest is the same as before:
- Mark exactly and drill as stated before in the exact size your next tool needs: This meens in the screws diameter for the piercer or in the first step of the hole cutter. This hole does not need to be deburred.
- the hole cutter is used as a normal drill but with very slow speeds. Take care, and clamp everything down very well!
- The piercer is simply placed and the screw turned until the material breaks and it comes loose again. Take care, you can ruin them with very thin metal sheets wich can bend and get stuck in there. You sometimes cannot get them out then without destroying the hole tool or at least the screw.
- You won't have a Countersink for these holes. Use a proper deburring tool if you have one or a knive with a small blade or needle files.
small rectangular Holes-Mark where you need the breakout. Do this VERY precisely again.
-Take your smallest drill, maximum 3mm. If the Item to be placed has a bit of a frame covering a bit of your mess you are lucky. Punch some guidance right onto all the corners of the breakout and drill as stated above. If there is no frame step back from the corners: 1/2 Diameter of your drill PLUS some extra 0.5mm for safety. Punch and drill.
- The inner of the breakout is then be drilled out, too. If you have a bit big enough choose as follows: smallest diameter of your breakout MINUS 1mm or better 2mm for beginners. Mark a center line, punch some guidance holes and drill. remember to stay a bit away from the sides to not ruin it! You can overlap the holes a bit, but don't overlap too much or your drill will get caught again and make a big mess.
- Grab your files and start filing. First every file that fits is ok to smooth out the holes. Then when you begin to get to the desired sides of the breakout a larger flat file helps a lot to give an even surface. Note that usually one small side of the flat file has teeth, too, and the other has not. Make use of this fact to get right into the corners.
Larger rectangular cutouts- mark again and do the corner holes as before.
- Option one: Take out the inner with a large drill as before. It takes more holes but works well. File down and you're done.
- Option two: If the breakout is really large you can take a Dremel like tool and start to work right on the desired edges. But this is very likely to make a mess if you don't have some practice. With plastics, take down the speed as low as possible! Don't give any pressure, the blade will cut its way. Else it will melt the workpiece. You may also try a nibbler as stated by others. Or a fret saw! That is a very precise tool. Can be used for small rectangular breakouts, too. Nearly nobody knows, but you can get metal cutting blades for these and they work a treat! Cheap too.
- Large breakouts in plastics I deburr with a cutter. Else I choose fine files or a deburring tool.
cutouts for Alignment pins- Drill the hole for the nominal diameter of the piece as stated above, NOT larger!
- Take a needle file and grind your way in by hand to make room for the pin(s).
Sounds like lots of efforts for a simple box? IT IS! But a nice box requieres at least the same and exact work as a good PCB and design. If it is skipped it will end in a mess.
Some general ideas for homeuse and cheaper working:
- if you don't have the workshop and room to do it, stick to plastics. You can even get metal cases with plastic fronts and backs. Plastic is easier to work with and the tools are cheaper in general. If you don't have a drill press you may even be able to get it right with an electric screwdriver.
- choose boxes with flat sheets of material to work on if you don't have the possibility of proper underfeeding and clamping. Parts in U-shape or L-shape are often hard to handle.
- have lots of scrapwood lying around your drillpress. This helps a lot when underfeeding, to clamp down without scratching the surface and so on.
- thin sheets of material can be supported with a flat piece of wood or plastic when drilling. Place it underneath and drill through your workpiece into that scrapwood. No warping!
- it is ok to choose the box after your design is finished. Actually I like to do it that way! You know exactly how much room you need inside. Also you know what elements you have on the outside. Choose a fitting box, then step back and go one size larger, if you don't have practice two sizes larger or even more. Trust me, you will need that room! Inside is less space, there are always some parts in there that get in the way, your external hardware reaches into the case a good bit... you get it. When arranging frontplates remember to leave room for some print, even if you don't actually print on there you will most likely want to write down some labels on there later. For one-off projects labels can be done with a labelprinter. These are cheap and work well. Labels on clear foil don't stick out too much but white foil gives always the right background to easily read the writing. It looks cleaner and more professional than written by hand. Just make sure to degrease before applying the labels and to align them very well. The Eye catches every mess there very well.