Applying high-pass and low-pass filters automatically

I have several audio files i want to apply the same filters.

Is there a way to apply these filter from the command line (so i can write a script to do it), or the GUI is the only way?

On the latter case, what would be the best strategy? When i apply them on several files at once, all of them end up with the duration of the longer one, by adding silence to them. What would be better, to apply the filters file by file, or to apply the filters in all of them, then remove the silence?

Have a look at SOX