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In a realistic design flow, circuit and system optimizations must interact with physical aspects of the design. For example, improvements in timing and power may require the replacement of large modules with variants that have different power/delay tradeoff, shape, and connectivity. New logic may be added late in the design flow, which is subject to interconnect optimization. To support such flexibility in design flows, we develop a robust system in performing Engineering Change Orders (ECOs). In contrast with the existing stand-alone tools that offer poor interfaces to the design flow and cannot handle a full range of modern very large scale integration layouts, our ECO-system reliably handles fixed objects and movable macros in instances with widely varying amounts of whitespace. It detects geometric regions and sections of the netlist that require modification and applies an adequate amount of change in each case. Given a reasonable initial placement, it applies minimal changes but is capable of replacing large regions to handle pathological cases. The ECO-system can be used in the range from high-level synthesis to physical synthesis and detail placement.