The software giant secured a federal court order to carry out the raids across the United States, accompanied by U.S. marshals, The Wall Street Journal reported.
Internet hosting sites in Denver, Dallas, Chicago, Seattle, Columbus, Ohio, Kansas City, Mo., and Scranton, Pa., were targeted.
In February, Microsoft filed a lawsuit in federal court in Seattle against unnamed operators of the "Rustock botnet," a global network of computers infected with malicious software used to distribute vast amounts of spam selling everything from pirated software to prescription drugs.
Richard Boscovich, senior attorney in Microsoft's digital crimes unit, said the operation seemed to be "100 percent effective."
The court authorized Microsoft to seize "command-and-control" machines through which the botnet operators sent instructions to more than a million hijacked computers worldwide. Most of them are owned by people unaware that their computers were taken over by outsiders.
The Rustock botnet was responsible for almost half the world's spam last year, the security firm Symantec Corp. stated in a blog post Thursday.
The unknown defendants are called "John Does 1-11."