From LQWiki

A clean room is a containament-free laboratory where work is done of sensitive equipment, including electronics.

The term is also used in a metaphorical sense to describe the process by which a clone of a product can be created that doesn't violate copyrights or patents of the company that makes the original product. For example, if a group of people wanted to clone a copyrighted piece of software, they would split into two groups. One group would reverse engineer the original program, and write a specification describing what the program does, and what a new program would have to do in order to be compatible. The second group then writes the clone based on the specification written by the first group, without ever having looked at the original program.