The only way to transform to native x64 code is to be in possesion of the source code and the developpement environment is was made on. The satndard x86 code runs just fine under the WOW and there is no gain to be made if the code is not going to use the extended registres and memory usage available in the x64 world. So usualy this requires a total review of the source code.
Besides that the only pace where it is mandatory to use it is for Device Drivers and that is reserved to very specialized programmers.
Arcadi