I agree with annccodeal, but to amplify a little bit, on Xilinx, there may be a few ways to do this. The XDL file format allows (or used to allow) explicit placement and routing. In addition, it should be possible to script the FPGA Editor to implement custom routing.
As regards placement, there is a rich infrastructure to constrain technology mapping of logic to primitives and to control placement of those primitives. For example LUT_MAP constraints can control technology mapping and LOC and RLOC constraints can determine placement. In practice, these allow the experienced designer great control over how a design is implemented without requiring them to duplicate man-centuries of software development to generate a bitstream directly.
You may also find interesting the current state of the art FPGA CAD research software such VPR. In my opinion these are challenged to keep up with vendor's own tools that must cope with modern heterogeneous FPGAs with splittable 6-LUTs, DSP blocks, etc.
Happy hacking.