besides the aforementioned ant task you can use a user defined builder in eclipse to preprocess files with a preprocessor. run->external tools->external tools->program->new
under the main tab:
location: path to your preprocessor
working directory: $(container_loc)
arguments: -w -Wall -C -o${container_loc}\preprocessed\${resource_name} ${resource_loc}

refresh: check refresh resources upon completion

now under project->properties->builders->import->(your preprocessor tool)

or if you want to omit the run thingy

project->properties->builders->new

personally i'd prefer the specialized ant task or a complete nature with customized builders within eclipse, which makes it possible to use whatever "toolchain" you're using :-)

kind regards,
rené