Botnets are a pervasive threat to the Internet and its inhabitants. A botnet is a collection of infected machines that receive commands from the botmaster, a person, group or nation- state, to perform malicious actions. Instead of “cleaning” individual infections, one can sever the method of communication between a botmaster and her zombies by attempting a botnet takedown, which contains the botnet and its malicious actions. Unfortunately, takedowns are currently performed without technical rigor nor are there automated and independent means to measure success or assist in performing them. This dissertation focuses on understanding the criminal infrastructure that enables communication between a botmaster and her zombies in order to measure attempts at, and to perform, successful takedowns. We show that by interrogating malware and performing large-scale analysis of passively collected network data, we can measure if a past botnet takedown was successful and use the same techniques to perform more comprehensive takedowns in the future.