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The physical design will 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.
Some PCB design packages will let you specify 3D models for components and then output the board as a CAD object. This is useful if the design needs to be really precise about clearances.
Mechanical engineering with solidworks is a different skillset and profession. As it is said, the design has to proceed in parallel with communication between the two designers.
Generally, 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.
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