I have some mpeg film files with subtitles on,if i re-encode them will i be able to remove the subs,if so which program is the best for it.

if they are just stand alone mpeg files, then no you can just "remove" them as they have been encoded into the video stream.
A bit of a extreme solution would be to clip the movie just above where the subs are, but that might be a fair chunk off the bottom of the picture.
If you did want to do this then tmpgenc can do this for you.