How to make a nice PCB enclosure for a product?
No, your PCB is not "ready" if you haven't got the mechanical constraints yet!

Since PCBs can be made in almost any shape, you figure out how much board area you need, then start with the mechanical design.  Having the PCB done and then looking for a box is comletely backwards.  Unless this is a very high volume product, you are much better off using some off the shelf case.

For very low volumes, you buy the standard box and mill and drill the cutouts yourself or have a local machine shop do it.  For higher volumes (usually a few 100), the box companies will usually customize their standard products with holes and cutouts according to your specs.  They do this with a modified mold, so in volume this is cheaper than machining the custom stuff afterwards.

There are many box companies out there.  We keep a few of different sized boxes around for one-off projects.  We have Eagle board outline templates for boxes we use regularly, like the Unibox #128.