After PCB layout

First things first. You do not, repeat not, wait until the board is laid out to design the enclosure. Not if you want to be a professional.

The circuit designer must work closely with the mechanical designer. For equipment incorporating pcbs, the following need to be considered: power supply location and dimensions, thermal limits (both from the board AND the power supply), cable routing, exterior connector choice and placement, EMI shielding (considering EMI in both directions), external access and mounting, and potentially other effects as well. All of these things can bite you on the butt if you ignore them, and any of them may well impact the board dimensions and layout.

Typically this is an iterative, back-and-forth process. The mechanical designer (or designers) will say "This is what you've got to work with." The electrical says, "Nope. Won't work. I need more room for cables/waste heat/board area/etc". Mechanical says, "Well, how about if we do such-and such", and the conversation keeps up until either an accommodation is reached, or it becomes clear that something has to give in the system requirements, at which time the problem gets bounced to the managers.

Only once the two sides are in agreement can the board layout begin, and details of board geometry are dealt with via CAD, as the board physical design is integrated with the enclosure.

EDIT - It occurs to me that my above discussion may be a bit idealistic. It is certainly possible that, in some organizations, the layout requirements are presented as a fait accompli. For instance, marketing has decreed that the latest version of the circuit (which requires much more functionality) must fit into the existing boxes. And, of course, the new circuit must cost less than the old version. In this sort of situation, a good designer may well rise to the occasion - or maybe not. In either case, it's probably a good idea to update your resume. If you fail, you may well get canned. If you succeed, you know that management is going to do it again and again until you do fail. Either way, it's time to look elsewhere.

In general, the placement of input and output connections on a PCB is dictated at least in part by the enclosure design. This means that the enclosure design needs to be completed BEFORE you do the physical layout of the PCB.

The physical design will generally be done in a drafting package such as AutoCAD or SolidWorks, and one of the outputs from this process will be the "outline drawing" for the PCB. This will specify all of the points where the PCB interacts in some way with its mechanical environment: the placement of controls and indicators, I/O connectors, mounting holes and the dimensions/shape of the board itself. This drawing, plus the schematic and bill of materials, becomes the input to the PCB layout process.

Above Posts answer clearly the procedure ,but in Big companies or for mass production.For small/medium companies or special projects that does not produced in large quantities ,usually designers estimate products needed space,then buy a appropriate Box equipped with necessary In/Out ports and based on it designed a PCB ,this saved a lot of money in production for small/medium quantities.