This paper presents a new approach to timing optimization for FPGA designs, namely incremental physical resynthesis, to answer the challenge of effectively integrating logic and physical optimizations without incurring unmanageable runtime complexity. Unlike previous approaches to this problem which limit the types of operations and/or architectural features, we take advantage of many architectural characteristics of modern FPGA devices, and utilize many types of optimizations including cell repacking, signal rerouting, resource retargeting, and logic restructuring, accompanied by efficient incremental placement, to gradually transform a design via a series of localized logic and physical optimizations that verifiably improve overall compli...