to clear just the search history without clearing all your other autofill information you have to do it one at a time.
click in the box where you want to clear the history, press the down arrow on the keyboard and then press delete and the first one will go... press delete again and the second one will go... repeat until all clear.
or if you have google toolbar or a google search in your browser menu search then right click on the google logo next to the search box and select clear history.