I’ve been talking quite a bit about using ArcPy and Python as a means to go back to using the command line for GIS analysis. You get such a better understanding as to what you are doing with the geospatial analysis functions when you type them in manually rather than using a wizard.
There are other ways to do this though. Darren Cope has a short blog post on using OGR for clipping GIS data files. Simple and sweet!
It’s just that easy, and best of all it just works when all other methods fail!
That’s just it though, command line usually works when GUI’s fail. The logical outcome is stop using the darn GUI!