The way I do it is simply pull as lightly as possible on the stems and they come out without much disturbance of the lower dirt bed. It really isn't messy it settles in and the addition of the red clay aids in ridding the dirt of its buoyancy. There really is a tangible difference in plant health of heavy root feeders like my apontogens, ruffled swords and crypts. I would highly recommend doing it and coming from someone who was equally intimidated at the thought of a dieted tank, don't be. The horror stories that people tell about dirtied substrates are 90% of the time due to their own lack of planning.
This was the article that I used as my guide:
http://gwapa.org/wordpress/articles/mineralized-soil-substrate/