See clean up, def. 1.
Empty something of its contents, leave bare. For example, The crows cleaned out the whole field of corn, or At the shop's first sale the customers cleaned out the entire stock of shoes. [Mid-1800s]
Deprive of money or other material resources. This usage originated in gambling, where it signified losing one's last stake. Charles Dickens had it in Oliver Twist (1838): "He has cleaned me out, but I can go and earn some more." [Early 1800s]
Drive out by force, as in The new CEO tried to get away with cleaning out all employees over the age of 60. [Mid-1800s]