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whatever you are doing in pcb, will be done in silicon incase of physical design. you will probably be designing the traces. here, ppl r designing masks which will be used during semiconductor processing.
processing involves creation of openings on a layer laid above the silicon. This layer is called mask, which can be removed by means of chemicals.
some parts of it are exposed to the UV light and some parts are not. The parts which are not exposed to UV light will be dissolved by chemicals. When the same chemical is applied to the parts exposed to light, they will not dissolve. So, this leaves some areas of silicon open for further processing and some are not.
The silicon used as substrate will not have any n or p junctions. it ll be a insulating substrate. Now, some parts of the silicon are uncovered and some are covered. The uncovered parts will be diffused with boron or phosporous so as to make them into n or p type materials, essential components for making a transistor.
The abstracted process of making this mask is called physical design.