Milkyway library means the design in layout format and you need the reference milkyway library to create your layout design. Reference milkyway library consists the predesigned layout of basic cells like AND, OR, NAND so on. Milkway is a term used in Synopsys tool, but different vendors(like cadence) have different names for their layout libraries and views.
In PnR , we give gate-level netlist as input to layout tool. This netlist has only logical information that how the cells are connected but no physical information. In layout you actually give information about std. cell's height, their pins location (by loading the reference library), based on logical and physical information tool place and route the design.