The Organic Sweep is the final part of the Irken Empire's movement against any planet marked for conquest by the Almighty Tallest. After one of the Invaders successfully undermines the defenses of their assigned planet, the ships in the Armada position themselves over the targeted planet and bombard its surface with all of their artillery. The end result is devastating - all life on the surface is exterminated, and any structures are thoroughly eradicated. In Battle of the Planets, Irken ships could be seen burning a massive Irken insignia into the Planet Blorch's surface with lasers. This may or may not be standard procedure.
Not all of the motives behind the Organic Sweep have been completely defined (although, according to Invader Skoodge, it is "so that no Irken boot has to come into contact with any unsavory alien filth"), though its main purpose is apparent: to reduce the surface of a conquered planet into flat ground, clearing the way for Irkens to begin terraforming.
Possible motives behind the Organic Sweep include the apparent xenophobic tendencies of the Irken race; they do indeed believe themselves to be superior to any and all other life forms. Erasing them from existence may simply be the confirmation they desire and reduce contact with "inferior" species; alternately, it may simply be because creatures such as the Blorchians are primitive and not intelligent enough to enslave for manual labor.
The Organic Sweep is carried out after an Irken Invader successfully undermines the planet's defenses, likely to eliminate any sort of retaliation against the approaching fleet. According to Skoodge, the Invader responsible for the conquering of the planet fires the first cannon.