Originally, these flows were molten throughout.  Cooling of the rock caused shrinking, resulting in horizontal tensions which in turn caused the lava surface to crack into polygonal patterns.  This is similar to shapes produced on a mud flat as it dries in the sun.  As the cooling progressed deeper into the flow, so did the shrinkage; as a consequence, the surface cracks extended deeper and deeper into the lava as well producing the columns we see today. 
  
The Columns of the Giants were formed before the last ice age.  There were several periods of glaciation after the birth of the columns and these glaciers "carved" the original five square miles of basaltic mass down to the present two square mile area.  With the passing of the ice age, the ice melted, leaving only the scars of glaciation.  Then three or four thousand years ago, ice began to accumulate in the Sierras once more.  Geologist refer to this as "The Little Ice Age."  This age has passed its peak and the ice fields are slowly retreating.  However, in this area, evidence of this ice age can still be found.  As the giant columns broke and fell, the resulting talus slope covered up and helped preserve remnants of these ice fields.  Today this field is replenished each year by the winter snow and cold temperatures.  During the summer you can feel the cold breezes coming up through the talus material from the ice field below.  These cold breezes create a natural refrigerator among the rocks. 

-- The above Information is from a US Forest Service plaque at the Columns of the Giants
 
 
Links:
USDA Forest Service - Stanislaus National Forest
Devils Postpile National Monument - similar geologic formations